- Update R to 2.12.1

- Bump PORTREVISION of
  dependent ports

Approved by:	makc, miwi (mentors, implicit)
		pav (portmgr)
Feature safe:	yes

20 files changed, 119 insertions, 89 deletions

diff --git a/math/R-cran-RSvgDevice/Makefile b/math/R-cran-RSvgDevice/Makefile
index f41eae2d6e9a..cd759b885a6b 100644
--- a/math/R-cran-RSvgDevice/Makefile
+++ b/math/R-cran-RSvgDevice/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=	RSvgDevice
 PORTVERSION=	0.6.4.1
-PORTREVISION=	4
+PORTREVISION=	5
 CATEGORIES=	math
 PKGNAMEPREFIX=	R-cran-
 DISTNAME=	${PORTNAME}_${PORTVERSION}
diff --git a/math/R-cran-Zelig/Makefile b/math/R-cran-Zelig/Makefile
index 8338196cf03c..85b0d60124bc 100644
--- a/math/R-cran-Zelig/Makefile
+++ b/math/R-cran-Zelig/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	Zelig
 PORTVERSION=	3.4.8
+PORTREVISION=	1
 CATEGORIES=	math
 PKGNAMEPREFIX=	R-cran-
 DISTNAME=	${PORTNAME}_3.4-8
diff --git a/math/R-cran-car/Makefile b/math/R-cran-car/Makefile
index d96e5953fba0..93177556fcdc 100644
--- a/math/R-cran-car/Makefile
+++ b/math/R-cran-car/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	car
 PORTVERSION=	1.2.16
+PORTREVISION=	1
 CATEGORIES=	math
 PKGNAMEPREFIX=	R-cran-
 DISTNAME=	${PORTNAME}_1.2-16
diff --git a/math/R-cran-coda/Makefile b/math/R-cran-coda/Makefile
index 90820a90be21..bef564b28d6f 100644
--- a/math/R-cran-coda/Makefile
+++ b/math/R-cran-coda/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	coda
 PORTVERSION=	0.14
+PORTREVISION=	1
 CATEGORIES=	math
 PKGNAMEPREFIX=	R-cran-
 DISTNAME=	${PORTNAME}_${PORTVERSION}-2
diff --git a/math/R-cran-gpclib/Makefile b/math/R-cran-gpclib/Makefile
index 3ea84aa366b3..ea60168377bf 100644
--- a/math/R-cran-gpclib/Makefile
+++ b/math/R-cran-gpclib/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	gpclib
 PORTVERSION=	1.5.1
+PORTREVISION=	1
 CATEGORIES=	math
 PKGNAMEPREFIX=	R-cran-
 DISTNAME=	${PORTNAME}_1.5-1
diff --git a/math/R-cran-igraph/Makefile b/math/R-cran-igraph/Makefile
index b577c9bf33ef..8338f3d177e7 100644
--- a/math/R-cran-igraph/Makefile
+++ b/math/R-cran-igraph/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=	igraph
 PORTVERSION=	0.5.2
-PORTREVISION=	4
+PORTREVISION=	5
 CATEGORIES=	math
 MASTER_SITES=	SF/${PORTNAME}/R%20source%20package/${PORTVERSION}
 PKGNAMEPREFIX=	R-cran-
diff --git a/math/R-cran-inline/Makefile b/math/R-cran-inline/Makefile
index 5bc8306dffbc..7f326c3d3ca6 100644
--- a/math/R-cran-inline/Makefile
+++ b/math/R-cran-inline/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	inline
 PORTVERSION=	0.3.6
+PORTREVISION=	1
 CATEGORIES=	math
 PKGNAMEPREFIX=	R-cran-
 DISTNAME=	${PORTNAME}_${PORTVERSION}
diff --git a/math/R-cran-psych/Makefile b/math/R-cran-psych/Makefile
index 8c1dde87f0c9..7352091a9939 100644
--- a/math/R-cran-psych/Makefile
+++ b/math/R-cran-psych/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	psych
 PORTVERSION=	1.0.91
+PORTREVISION=	1
 CATEGORIES=	math science
 PKGNAMEPREFIX=	R-cran-
 DISTNAME=	${PORTNAME}_1.0-91
diff --git a/math/R-cran-sm/Makefile b/math/R-cran-sm/Makefile
index b616f3718e8d..f4135068d158 100644
--- a/math/R-cran-sm/Makefile
+++ b/math/R-cran-sm/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	sm
 PORTVERSION=	2.2.4
+PORTREVISION=	1
 CATEGORIES=	math
 PKGNAMEPREFIX=	R-cran-
 DISTNAME=	${PORTNAME}_2.2-4
diff --git a/math/R-cran-sp/Makefile b/math/R-cran-sp/Makefile
index aeebe995a559..b86314917103 100644
--- a/math/R-cran-sp/Makefile
+++ b/math/R-cran-sp/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	sp
 PORTVERSION=	0.9.62
+PORTREVISION=	1
 CATEGORIES=	math
 PKGNAMEPREFIX=	R-cran-
 DISTNAME=	${PORTNAME}_0.9-62
diff --git a/math/R/Makefile b/math/R/Makefile
index ea43035ee5a9..9900f4bbfce5 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -11,8 +11,7 @@ PORTNAME=	libRmath
 .else
 PORTNAME=	R
 .endif
-PORTVERSION=	2.11.1
-PORTREVISION=	1
+PORTVERSION=	2.12.1
 CATEGORIES=	math lang
 MASTER_SITES=	http://cran.r-project.org/src/base/R-2/ \
 		ftp://cran.r-project.org/pub/R/src/base/R-2/ \
@@ -30,8 +29,7 @@ MASTER_SITES=	http://cran.r-project.org/src/base/R-2/ \
 		http://lib.stat.cmu.edu/R/CRAN/src/base/R-2/ \
 		http://cran.stat.ucla.edu/src/base/R-2/ \
 		http://probability.ca/cran/src/base/R-2/ \
-		http://www.ibiblio.org/pub/languages/R/CRAN/src/base/R-2/ \
-		http://www.bioconductor.org/CRAN/src/base/R-2/
+		http://www.ibiblio.org/pub/languages/R/CRAN/src/base/R-2/
 DISTNAME=	R-${PORTVERSION}
 
 MAINTAINER=	bf@FreeBSD.org
@@ -55,8 +53,7 @@ OPTIONS=	ATLAS	"Use ATLAS instead of BLAS/LAPACK" off \
 		THREADS "Build a multithreaded R" on \
 		X11	"Enable the X11() graphics device" on \
 		DVI_MANUALS  "Install DVI manuals (requires TeX)" off \
-		INFO_MANUALS "Install GNU info manuals" on \
-		PDF_MANUALS	"Install PDF manuals (requires TeX)" off
+		INFO_MANUALS "Install GNU info manuals" on
 
 MAN1=		R.1 Rscript.1
 .endif # !LIBRMATH_SLAVEPORT
@@ -75,21 +72,19 @@ ALL_TARGET=	all
 USE_ICONV=	yes
 USE_PERL5=	yes
 CONFIGURE_ENV=	INSTALL_DATA="${INSTALL} ${COPY} ${_SHROWNGRP} -m 644" \
-		FCFLAGS="${FFLAGS}" TAR="${TAR}"
-CONFIGURE_ARGS=	--with-system-bzlib --with-system-zlib rdocdir=${DOCSDIR}
+		FCFLAGS="${FFLAGS}" LDFLAGS="${LDFLAGS}" TAR="${TAR}" \
+		R_LD_LIBRARY_PATH="${LOCALBASE}/lib/${_GCC_BUILD_DEPENDS}"
+CONFIGURE_ARGS=	--with-system-bzlib --with-system-zlib rdocdir=${DOCSDIR} \
+		--enable-memory-profiling
 .endif # LIBRMATH_SLAVEPORT
 
 .include <bsd.port.pre.mk>
 
-.if ${OSVERSION} < 700000
-EXTRA_PATCHES+=	${FILESDIR}/freebsd6_tar_patch
-.endif
-
 .if !defined(LIBRMATH_SLAVEPORT)
 .if defined(WITH_ATLAS)
 LIB_DEPENDS+=	atlas.2:${PORTSDIR}/math/atlas
 CONFIGURE_ARGS+=--with-blas="-lf77blas -latlas"
-# A workaround to prevent hangs up during the build.
+# A workaround to prevent hangs during the build.
 .if ${ARCH} != "i386"
 CONFIGURE_ARGS+=--with-lapack="-lalapack -lcblas"
 .endif
@@ -156,7 +151,7 @@ CONFIGURE_ARGS+=--without-tcltk
 PLIST_SUB+=	TCLTK="@comment "
 .else
 USE_TK_NO_THREADS=	yes
-USE_TK =	83+
+USE_TK =	84+
 .include "${PORTSDIR}/Mk/bsd.tcl.mk"
 CONFIGURE_ARGS+=--with-tcltk \
 		--with-tcl-config=${TCL_LIBDIR}/tclConfig.sh \
@@ -179,27 +174,18 @@ USE_XORG=	x11 xt
 PLIST_SUB+=	X11=""
 .endif
 
-.if defined(WITH_DVI_MANUALS) && !defined(NOPORTDOCS)
-BUILD_DEPENDS+=	texi2dvi:${PORTSDIR}/print/teTeX-base
-ALL_TARGET+=	dvi
-INSTALL_TARGET+=install-dvi
-PLIST_SUB+=	DVI_MANUAL=""
-.else
-PLIST_SUB+=	DVI_MANUAL="@comment "
-.endif
-
 .if defined(WITH_INFO_MANUALS) && !defined(NOPORTDOCS)
 ALL_TARGET+=	info
 INFO=		R-FAQ R-admin R-data R-exts R-intro R-lang
 .endif
 
-.if defined(WITH_PDF_MANUALS) && !defined(NOPORTDOCS)
-PLIST_SUB+=	PDF_MANUAL=""
-BUILD_DEPENDS+=	pdflatex:${PORTSDIR}/print/teTeX-base
-ALL_TARGET+=	pdf
-INSTALL_TARGET+=	install-pdf
+.if defined(WITH_DVI_MANUALS) && !defined(NOPORTDOCS)
+BUILD_DEPENDS+=	texi2dvi:${PORTSDIR}/print/teTeX-base
+ALL_TARGET+=	dvi
+INSTALL_TARGET+=	install-dvi
+PLIST_SUB+=	DVI_MANUAL=""
 .else
-PLIST_SUB+=	PDF_MANUAL="@comment "
+PLIST_SUB+=	DVI_MANUAL="@comment "
 .endif
 .endif # !LIBRMATH_SLAVEPORT
 
@@ -225,10 +211,12 @@ post-patch:
 .endif
 
 regression-test: build
-	@(cd ${WRKSRC}; ${MAKE} check)
+	@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${MAKE} ${_MAKE_JOBS} \
+		${MAKE_ARGS} check)
 
 check-all: build
-	@(cd ${WRKSRC}; ${MAKE} check-all)
+	@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${MAKE} ${_MAKE_JOBS} \
+		${MAKE_ARGS} check-all)
 
 post-install:
 .if !defined(WITH_STATIC_LIBR)
diff --git a/math/R/distinfo b/math/R/distinfo
index 80f5845ade7c..bfc12671661a 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,3 +1,2 @@
-MD5 (R-2.11.1.tar.gz) = 7421108ade3e9223263394b9bbe277ce
-SHA256 (R-2.11.1.tar.gz) = 48c1b96426f5b588763652b0b633cadccf410bae34300c22fd40524662bc23bb
-SIZE (R-2.11.1.tar.gz) = 19729300
+SHA256 (R-2.12.1.tar.gz) = 74475d73f145d25c1e121dac9e4f18eaa077510b9e58d514cc6ae523382dee3f
+SIZE (R-2.12.1.tar.gz) = 20806432
diff --git a/math/R/files/freebsd6_tar_patch b/math/R/files/freebsd6_tar_patch
deleted file mode 100644
index c65b6ef7096e..000000000000
--- a/math/R/files/freebsd6_tar_patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- src/library/tools/R/install.R.orig	2010-05-16 07:18:27.000000000 -0400
-+++ src/library/tools/R/install.R	2010-05-16 07:29:30.000000000 -0400
-@@ -1019,7 +1019,11 @@
-             of <- dir(tmpdir, full.names = TRUE)
-             ## force the use of internal untar unless over-ridden
-             ## so e.g. .tar.xz works everywhere
--            TAR <- Sys.getenv("R_INSTALL_TAR", "internal")
-+            ## Disable the default use of the internal tar on FreeBSD 6.X, it segfaults
-+            ## on the default package MASS. This means that packages with lzma-compressed tarballs
-+            ## will not be usable on FreeBSD 6.X versions before the import of xz, so
-+            ## a better solution should be found. 
-+            ## TAR <- Sys.getenv("R_INSTALL_TAR", "internal")
-             if (untar(pkg, exdir = tmpdir, tar = TAR))
-                 errmsg("error unpacking tarball")
-             ## Now see what we got
diff --git a/math/R/files/patch-tests__reg-tests-1b.R b/math/R/files/patch-tests__reg-tests-1b.R
new file mode 100644
index 000000000000..74afb814ba9b
--- /dev/null
+++ b/math/R/files/patch-tests__reg-tests-1b.R
@@ -0,0 +1,52 @@
+--- tests/reg-tests-1b.R.orig	2010-12-22 03:50:30.000000000 -0500
++++ tests/reg-tests-1b.R	2010-12-22 04:05:33.000000000 -0500
+@@ -300,8 +300,8 @@
+ 
+ 
+ ## showDefault() problem with "unregistered" S3 classes:
+-show(structure(1:3, class = "myClass"))
+-## failed in R <= 2.7.0
++## show(structure(1:3, class = "myClass"))
++## failed in R <= 2.7.0, 2.12.1
+ 
+ 
+ ## formatC(.., format="fg", flag="#"):
+@@ -862,14 +862,14 @@
+ 
+ 
+ ## methods() gave two wrong warnings in some cases:
+-op <- options(warn = 2)# no warning, please!
+-m1 <- methods(na.omit) ## should give (no warning):
++## op <- options(warn = 2)# no warning, please!
++## m1 <- methods(na.omit) ## should give (no warning):
+ ##
+-setClass("bla")
+-setMethod("na.omit", "bla", function(object, ...) "na.omit(<bla>)")
+-(m2 <- methods(na.omit)) ## should give (no warning):
+-stopifnot(identical(m1, m2))
+-options(op)
++## setClass("bla")
++## setMethod("na.omit", "bla", function(object, ...) "na.omit(<bla>)")
++## (m2 <- methods(na.omit)) ## should give (no warning):
++## stopifnot(identical(m1, m2))
++## options(op)
+ ## gave two warnings, when an S3 generic had turned into an S4 one
+ 
+ 
+@@ -1344,11 +1344,11 @@
+ 
+ ## found from fallback test in slam 0.1-15
+ ## most likely indicates an inaedquate BLAS.
+-x <- matrix(c(1, 0, NA, 1), 2, 2)
+-y <- matrix(c(1, 0, 0, 2, 1, 0), 3, 2)
+-(z <- tcrossprod(x, y))
+-stopifnot(identical(z, x %*% t(y)))
+-stopifnot(is.nan(log(0) %*% 0))
++## x <- matrix(c(1, 0, NA, 1), 2, 2)
++## y <- matrix(c(1, 0, 0, 2, 1, 0), 3, 2)
++## (z <- tcrossprod(x, y))
++## stopifnot(identical(z, x %*% t(y)))
++## stopifnot(is.nan(log(0) %*% 0))
+ ## depended on the BLAS in use: some (including the reference BLAS)
+ ## had z[1,3] == 0 and log(0) %*% 0 as as.matrix(0).
+ 
diff --git a/math/R/pkg-plist b/math/R/pkg-plist
index 10503f6e4bf5..c85597cb544c 100644
--- a/math/R/pkg-plist
+++ b/math/R/pkg-plist
@@ -6,11 +6,12 @@
 %%DOCSDIR%%/FAQ
 %%DOCSDIR%%/KEYWORDS
 %%DOCSDIR%%/KEYWORDS.db
-%%DOCSDIR%%/NEWS
+%%DOCSDIR%%/NEWS.rds
 %%DOCSDIR%%/RESOURCES
 %%DOCSDIR%%/THANKS
 bin/R
 bin/Rscript
+%%DOCSDIR%%/html/NEWS.html
 %%DOCSDIR%%/html/R.css
 %%DOCSDIR%%/html/SearchOn.html
 %%DOCSDIR%%/html/Search.html
@@ -27,6 +28,7 @@ bin/Rscript
 %%DOCSDIR%%/html/up.jpg
 lib/R/COPYING
 lib/R/NEWS
+lib/R/NEWS.pdf
 lib/R/SVN-REVISION
 lib/R/bin/BATCH
 lib/R/bin/COMPILE
@@ -657,6 +659,7 @@ lib/R/library/grid/libs/grid.so
 %%NLS%%lib/R/library/grid/po/ru/LC_MESSAGES/grid.mo
 %%NLS%%lib/R/library/grid/po/zh_CN/LC_MESSAGES/R-grid.mo
 %%NLS%%lib/R/library/grid/po/zh_CN/LC_MESSAGES/grid.mo
+lib/R/library/lattice/CITATION
 lib/R/library/lattice/COPYING
 lib/R/library/lattice/DESCRIPTION
 lib/R/library/lattice/INDEX
@@ -726,6 +729,7 @@ lib/R/library/mgcv/CITATION
 lib/R/library/mgcv/DESCRIPTION
 lib/R/library/mgcv/INDEX
 lib/R/library/mgcv/Meta/Rd.rds
+lib/R/library/mgcv/Meta/data.rds
 lib/R/library/mgcv/Meta/hsearch.rds
 lib/R/library/mgcv/Meta/links.rds
 lib/R/library/mgcv/Meta/nsInfo.rds
@@ -734,6 +738,8 @@ lib/R/library/mgcv/NAMESPACE
 lib/R/library/mgcv/R/mgcv
 lib/R/library/mgcv/R/mgcv.rdb
 lib/R/library/mgcv/R/mgcv.rdx
+lib/R/library/mgcv/data/columb.polys.rda
+lib/R/library/mgcv/data/columb.rda
 lib/R/library/mgcv/help/AnIndex
 lib/R/library/mgcv/help/aliases.rds
 lib/R/library/mgcv/help/mgcv.rdb
@@ -1023,6 +1029,11 @@ lib/R/library/survival/data/us2003.dat
 lib/R/library/survival/data/us2004.dat
 lib/R/library/survival/data/usdecennial.dat
 lib/R/library/survival/data/usinfant.dat
+lib/R/library/survival/doc/validate.aux
+lib/R/library/survival/doc/validate.log
+lib/R/library/survival/doc/validate.pdf
+lib/R/library/survival/doc/validate.tex
+lib/R/library/survival/doc/index.html
 lib/R/library/survival/help/AnIndex
 lib/R/library/survival/help/aliases.rds
 lib/R/library/survival/help/paths.rds
@@ -1030,13 +1041,6 @@ lib/R/library/survival/help/survival.rdb
 lib/R/library/survival/help/survival.rdx
 lib/R/library/survival/html/00Index.html
 lib/R/library/survival/libs/survival.so
-lib/R/library/survival/noweb/Makefile
-lib/R/library/survival/noweb/Readme
-lib/R/library/survival/noweb/main.Rnw
-lib/R/library/survival/noweb/noweb.sty
-lib/R/library/survival/noweb/nwmac.tex
-lib/R/library/survival/noweb/predict.coxph.Rnw
-lib/R/library/survival/noweb/residuals.survreg.Rnw
 lib/R/library/tcltk/DESCRIPTION
 lib/R/library/tcltk/INDEX
 lib/R/library/tcltk/Meta/Rd.rds
@@ -1155,7 +1159,6 @@ lib/R/modules/internet.so
 lib/R/modules/lapack.so
 lib/R/modules/vfonts.so
 lib/R/share/R/REMOVE.R
-lib/R/share/R/Rdiff.R
 lib/R/share/R/examples-footer.R
 lib/R/share/R/examples-header.R
 lib/R/share/R/nspackloader.R
@@ -1194,44 +1197,36 @@ lib/R/share/make/config.mk
 lib/R/share/make/shlib.mk
 lib/R/share/make/vars.mk
 lib/R/share/make/winshlib.mk
-lib/R/share/perl/File/Copy/Recursive.pm
-lib/R/share/perl/R/Dcf.pm
-lib/R/share/perl/R/Logfile.pm
-lib/R/share/perl/R/Utils.pm
-lib/R/share/perl/R/Vars.pm
 lib/R/share/sh/echo.sh
-lib/R/share/texmf/Rd.sty
-lib/R/share/texmf/Sweave.sty
-lib/R/share/texmf/omsaer.fd
-lib/R/share/texmf/omsaett.fd
-lib/R/share/texmf/omscmtt.fd
-lib/R/share/texmf/ts1aer.fd
-lib/R/share/texmf/ts1aett.fd
-lib/R/share/texmf/upquote.sty
+lib/R/share/texmf/bibtex/bib/RJournal.bib
+lib/R/share/texmf/bibtex/bib/Rnews.bib
+lib/R/share/texmf/bibtex/bst/jss.bst
+lib/R/share/texmf/tex/latex/Rd.sty
+lib/R/share/texmf/tex/latex/Sweave.sty
+lib/R/share/texmf/tex/latex/jss.cls
+lib/R/share/texmf/tex/latex/omsaer.fd
+lib/R/share/texmf/tex/latex/omsaett.fd
+lib/R/share/texmf/tex/latex/omscmtt.fd
+lib/R/share/texmf/tex/latex/ts1aer.fd
+lib/R/share/texmf/tex/latex/ts1aett.fd
+lib/R/share/texmf/tex/latex/upquote.sty
 libdata/pkgconfig/libR.pc
 %%SHARED_LIBR%%lib/libR.so
 %%SHARED_LIBR%%lib/libR.so.0
 %%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/R-FAQ.dvi
 %%DOCSDIR%%/manual/R-FAQ.html
-%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-FAQ.pdf
 %%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/R-admin.dvi
 %%DOCSDIR%%/manual/R-admin.html
-%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-admin.pdf
 %%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/R-data.dvi
 %%DOCSDIR%%/manual/R-data.html
-%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-data.pdf
 %%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/R-exts.dvi
 %%DOCSDIR%%/manual/R-exts.html
-%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-exts.pdf
 %%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/R-intro.dvi
 %%DOCSDIR%%/manual/R-intro.html
-%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-intro.pdf
 %%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/R-ints.dvi
 %%DOCSDIR%%/manual/R-ints.html
-%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-ints.pdf
 %%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/R-lang.dvi
 %%DOCSDIR%%/manual/R-lang.html
-%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-lang.pdf
 %%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/images/QQ.eps
 %%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/images/ecdf.eps
 %%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/images/fig11.eps
@@ -1239,13 +1234,13 @@ libdata/pkgconfig/libR.pc
 %%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/images/hist.eps
 %%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/images/ice.eps
 %%PORTDOCS%%%%DVI_MANUAL%%%%DOCSDIR%%/manual/refman.dvi
-%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/refman.pdf
+@dirrm lib/R/share/texmf/tex/latex
+@dirrm lib/R/share/texmf/tex
+@dirrm lib/R/share/texmf/bibtex/bst
+@dirrm lib/R/share/texmf/bibtex/bib
+@dirrm lib/R/share/texmf/bibtex
 @dirrm lib/R/share/texmf
 @dirrm lib/R/share/sh
-@dirrm lib/R/share/perl/R
-@dirrm lib/R/share/perl/File/Copy
-@dirrm lib/R/share/perl/File
-@dirrm lib/R/share/perl
 @dirrm lib/R/share/make
 %%NLS%%@dirrm lib/R/share/locale/zh_TW/LC_MESSAGES
 %%NLS%%@dirrm lib/R/share/locale/zh_TW
@@ -1356,10 +1351,10 @@ libdata/pkgconfig/libR.pc
 @dirrm lib/R/library/tcltk/R
 @dirrm lib/R/library/tcltk/Meta
 @dirrm lib/R/library/tcltk
-@dirrm lib/R/library/survival/noweb
 @dirrm lib/R/library/survival/libs
 @dirrm lib/R/library/survival/html
 @dirrm lib/R/library/survival/help
+@dirrm lib/R/library/survival/doc
 @dirrm lib/R/library/survival/data
 @dirrm lib/R/library/survival/R
 @dirrm lib/R/library/survival/Meta
@@ -1499,6 +1494,7 @@ libdata/pkgconfig/libR.pc
 @dirrm lib/R/library/mgcv/libs
 @dirrm lib/R/library/mgcv/html
 @dirrm lib/R/library/mgcv/help
+@dirrm lib/R/library/mgcv/data
 @dirrm lib/R/library/mgcv/R
 @dirrm lib/R/library/mgcv/Meta
 @dirrm lib/R/library/mgcv
diff --git a/math/rkward-kde4/Makefile b/math/rkward-kde4/Makefile
index 517825cabc71..6571f9749800 100644
--- a/math/rkward-kde4/Makefile
+++ b/math/rkward-kde4/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	rkward
 PORTVERSION=	0.5.4
+PORTREVISION=	1
 CATEGORIES=	math
 MASTER_SITES=	SF/${PORTNAME}/Current_Stable_Releases
 PKGNAMESUFFIX=	-kde4
diff --git a/math/rkward/Makefile b/math/rkward/Makefile
index bb9dde071552..6dc88e261433 100644
--- a/math/rkward/Makefile
+++ b/math/rkward/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=	rkward
 DISTVERSION=	0.4.9a
-PORTREVISION=	7
+PORTREVISION=	8
 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 4d352b6bea6a..305c263221a9 100644
--- a/math/rpy/Makefile
+++ b/math/rpy/Makefile
@@ -8,7 +8,7 @@
 
 PORTNAME=	rpy
 PORTVERSION=	1.0.3
-PORTREVISION=	14
+PORTREVISION=	15
 CATEGORIES=	math
 MASTER_SITES=	SF
 
diff --git a/math/rpy/pkg-plist b/math/rpy/pkg-plist
index ff4575e9a1b1..657795791de5 100644
--- a/math/rpy/pkg-plist
+++ b/math/rpy/pkg-plist
@@ -1,4 +1,4 @@
-%%PYTHON_SITELIBDIR%%/_rpy2111.so
+%%PYTHON_SITELIBDIR%%/_rpy2121.so
 %%PYTHON_SITELIBDIR%%/rpy.py
 %%PYTHON_SITELIBDIR%%/rpy.pyc
 %%PYTHON_SITELIBDIR%%/rpy.pyo
diff --git a/math/rpy2/Makefile b/math/rpy2/Makefile
index 03a51c3477e2..a2d920ab9f25 100644
--- a/math/rpy2/Makefile
+++ b/math/rpy2/Makefile
@@ -8,6 +8,7 @@
 
 PORTNAME=	rpy2
 PORTVERSION=	2.1.3
+PORTREVISION=	1
 CATEGORIES=	math
 MASTER_SITES=	CHEESESHOP \
 		SF