math/R: Update to version 3.3.2 and other changes

- Changes in version 3.3.2:
  https://cran.r-project.org/doc/manuals/r-release/NEWS.html

- Port Changes
    - Definitively set PORTNAME after removal of slave ports
    - Set MASTERS_SITES to CRAN
    - Make documentation installation simpler for users
        - make the DOCS option the only option for extra documentation
          (remove PDF option)
        - turn this option off by default since it pulls in over 1 GB of
          build dependencies (TeX and friends)
    - Do not make INFO option imply DOCS option
    - Cosmetic changes

Reviewed by:	mat
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8330

3 files changed, 390 insertions, 397 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index 0de59e0c3408..5ba7e4f69a4f 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -1,25 +1,10 @@
 # Created by: Maurice Castro <maurice@serc.rmit.edu.au>
 # $FreeBSD$
 
-PORTNAME?=		R
-PORTVERSION=		3.3.1
-PORTREVISION=		4
+PORTNAME=		R
+PORTVERSION=		3.3.2
 CATEGORIES=		math lang
-MASTER_SITES=		http://cran.r-project.org/%SUBDIR%/ \
-			ftp://cran.r-project.org/pub/R/%SUBDIR%/ \
-			http://cran.at.r-project.org/%SUBDIR%/ \
-			http://cran.au.r-project.org/%SUBDIR%/ \
-			http://cran.br.r-project.org/%SUBDIR%/ \
-			http://cran.ch.r-project.org/%SUBDIR%/ \
-			http://cran.es.r-project.org/%SUBDIR%/ \
-			http://cran.dk.r-project.org/%SUBDIR%/ \
-			http://cran.uk.r-project.org/%SUBDIR%/ \
-			http://cran.us.r-project.org/%SUBDIR%/ \
-			ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/%SUBDIR%/ \
-			http://lib.stat.cmu.edu/R/CRAN/%SUBDIR%/ \
-			http://cran.stat.ucla.edu/%SUBDIR%/ \
-			http://probability.ca/cran/%SUBDIR%/
-MASTER_SITE_SUBDIR=	src/base/R-${PORTVERSION:C|\..*||}
+MASTER_SITES=		CRAN/src/base/R-${PORTVERSION:C|\..*||}
 
 MAINTAINER=		jrm@FreeBSD.org
 COMMENT=		Language for statistical computing and graphics
@@ -35,14 +20,15 @@ CONFIGURE_ARGS=		--disable-java \
 GNU_CONFIGURE=		yes
 INSTALL_TARGET=		install-strip
 ONLY_FOR_ARCHS=		i386 amd64
-USES=			fortran iconv libtool localbase objc:compiler pathfix perl5 \
-			readline
+USES=			fortran iconv libtool localbase objc:compiler pathfix \
+			perl5 readline
+
 USE_PERL5=		build
 
-OPTIONS_DEFINE=		DOCS ICU INFO LDOUBLE LETTER LIBR MEMPROF NLS RPROF X11
+OPTIONS_DEFINE=		ICU INFO LDOUBLE LETTER LIBR MEMPROF NLS RPROF X11
 OPTIONS_GROUP=		NEEDGCC NEEDX11
 OPTIONS_GROUP_NEEDGCC=	LTO OPENMP
-OPTIONS_GROUP_NEEDX11=	GHOSTSCRIPT JPEG CAIROPANGO PDF PNG TCLTK TIFF
+OPTIONS_GROUP_NEEDX11=	ALLDOCS GHOSTSCRIPT JPEG CAIROPANGO PNG TCLTK TIFF
 OPTIONS_SINGLE=		BLAS
 OPTIONS_SINGLE_BLAS=	ATLAS OPENBLAS NETLIB RBLAS
 
@@ -51,6 +37,7 @@ OPTIONS_SUB=		YES
 ATLAS_DESC=		ATLAS BLAS implementation
 GHOSTSCRIPT_DESC=	Graphics device for bitmap files via Ghostscript
 CAIROPANGO_DESC=	Cairo graphics device and Pango multi-language text
+ALLDOCS_DESC=		All documentation (TeX build dependency)
 INFO_DESC=		GNU info manuals
 JPEG_DESC=		JPEG graphics device
 LDOUBLE_DESC=		Long double data type
@@ -62,7 +49,6 @@ NEEDGCC_DESC=		Require GCC
 NEEDX11_DESC=		Require X11
 NETLIB_DESC=		Netlib BLAS implementation
 OPENBLAS_DESC=		OpenBLAS BLAS implementation
-PDF_DESC=		PDF manuals (requires TeX)
 PNG_DESC=		PNG graphics device
 RBLAS_DESC=		Use R-bundled BLAS implementation
 RPROF_DESC=		R profiling via Rprof()
@@ -71,6 +57,12 @@ X11_DESC=		X11 graphics device
 OPTIONS_DEFAULT=	CAIROPANGO GHOSTSCRIPT ICU INFO JPEG LDOUBLE LIBR PNG \
 			RBLAS RPROF TCLTK TIFF X11
 
+ALLDOCS_BUILD_DEPENDS=	texi2any:print/texinfo
+.for i in KPSEWHICH MAKEINDEX PDFLATEX PDFTEX TEX TEXI2DVI
+ALLDOCS_CONFIGURE_ENV_OFF+=	ac_cv_path_${i}=""
+.endfor
+ALLDOCS_INSTALL_TARGET=	install-pdf
+ALLDOCS_USE=		tex=dvipsk:build,kpathsea:build,pdftex:build
 ATLAS_USES=		blaslapack:atlas
 ALTAS_CONFIGURE_ON=	--disable-BLAS-shlib
 ATLAS_VARS=		MANUAL_PACKAGE_BUILD=\
@@ -79,12 +71,11 @@ CAIROPANGO_IMPLIES=	X11
 CAIROPANGO_CONFIGURE_WITH=cairo
 CAIROPANGO_USES=	gettext jpeg pkgconfig
 CAIROPANGO_USE=		gnome=pango,cairo
-DOCS_BUILD_DEPENDS=	texi2any:print/texinfo
 GHOSTSCRIPT_IMPLIES=	X11
 GHOSTSCRIPT_USES=	ghostscript
 ICU_CONFIGURE_WITH=	ICU
 ICU_LIB_DEPENDS=	libicui18n.so:devel/icu
-INFO_IMPLIES=		DOCS
+INFO_BUILD_DEPENDS=	texi2any:print/texinfo
 INFO_INSTALL_TARGET=	install-info
 INFO_INFO=		R-FAQ R-admin R-data R-exts R-ints R-intro R-lang
 JPEG_IMPLIES=		X11
@@ -105,12 +96,6 @@ OPENBLAS_USES=		blaslapack:openblas
 OPENBLAS_CONFIGURE_ON=	--disable-BLAS-shlib
 OPENMP_CONFIGURE_ENABLE=openmp
 OPENMP_USE=		compiler:openmp
-PDF_IMPLIES=		DOCS X11
-PDF_USE=		tex=dvipsk:build,kpathsea:build,pdftex:build
-PDF_INSTALL_TARGET=	install-pdf
-.for i in KPSEWHICH MAKEINDEX PDFLATEX PDFTEX TEX TEXI2DVI
-PDF_CONFIGURE_ENV_OFF+=	ac_cv_path_${i}=""
-.endfor
 PNG_IMPLIES=		X11
 PNG_LIB_DEPENDS=	libpng.so:graphics/png
 PNG_CONFIGURE_WITH=	libpng
@@ -140,21 +125,29 @@ PLIST_SUB=		R_SOVERSION="${R_SOVERSION}" \
 .include <bsd.port.options.mk>
 .include "compiler.mk"
 
-# OPT_USE= ldconfig=${PREFIX}/lib/R/lib is broken.
-# It adds /lib/R/lib (without PREFIX) to ${PREFIX}/libdata/R.
 .if ${PORT_OPTIONS:MLIBR} || ${PORT_OPTIONS:MRBLAS}
 USE_LDCONFIG=		${PREFIX}/lib/R/lib
 .endif
 
 post-patch:
-	@${REINPLACE_CMD} -e "s|/usr/local|${LOCALBASE}|g" \
-		${WRKSRC}/configure
+	@${REINPLACE_CMD} -e "s|/usr/local|${LOCALBASE}|g" ${WRKSRC}/configure
 
+## TODO: Add missing soname and soversion to shared libraries
 post-install:
 .for L in R Rblas Rlapack
-	@if [ -d ${STAGEDIR}${PREFIX}/lib/R/lib ] ; then \
-	cd ${STAGEDIR}${PREFIX}/lib/R/lib; if [ -f lib${L}.so ] ; then \
-	${LN} -sf lib${L}.so lib${L}.so.${${L:tu}_SOVERSION} ; fi; fi
+	if [ -d ${STAGEDIR}${PREFIX}/lib/R/lib ]; then \
+		cd ${STAGEDIR}${PREFIX}/lib/R/lib; \
+		if [ -f lib${L}.so ]; then \
+			${LN} -sf lib${L}.so lib${L}.so.${${L:tu}_SOVERSION}; \
+		fi; \
+	fi
 .endfor
 
+post-install-ALLDOCS-off:
+	[ -n "${DOCSDIR}" ] && \
+		${RM} -r ${STAGEDIR}${DOCSDIR}/html && \
+		${RM} -r ${STAGEDIR}${DOCSDIR}/manual; \
+	${FIND} ${STAGEDIR}${PREFIX}/lib/R/library -type d \
+		\( -name html -or -name doc -or -name help \) -delete;
+
 .include <bsd.port.mk>
diff --git a/math/R/distinfo b/math/R/distinfo
index f63322597f89..596c17e603f0 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1470250856
-SHA256 (R-3.3.1.tar.gz) = 3dc59ae5831f5380f83c169bac2103ad052efe0ecec4ffa74bde4d85a0fda9e2
-SIZE (R-3.3.1.tar.gz) = 29848329
+TIMESTAMP = 1478005734
+SHA256 (R-3.3.2.tar.gz) = d294ad21e9f574fb4828ebb3a94b8cb34f4f304a41687a994be00dd41a4e514c
+SIZE (R-3.3.2.tar.gz) = 29440670
diff --git a/math/R/pkg-plist b/math/R/pkg-plist
index 91585053c4a7..498f8ae5228b 100644
--- a/math/R/pkg-plist
+++ b/math/R/pkg-plist
@@ -8,20 +8,21 @@
 %%DOCSDIR%%/NEWS.rds
 %%DOCSDIR%%/RESOURCES
 %%DOCSDIR%%/THANKS
-%%DOCSDIR%%/html/NEWS.html
-%%DOCSDIR%%/html/R.css
-%%DOCSDIR%%/html/SearchOn.html
-%%DOCSDIR%%/html/Search.html
-%%DOCSDIR%%/html/about.html
-%%DOCSDIR%%/html/favicon.ico
-%%DOCSDIR%%/html/index.html
-%%DOCSDIR%%/html/left.jpg
-%%DOCSDIR%%/html/logo.jpg
-%%DOCSDIR%%/html/packages-head-utf8.html
-%%DOCSDIR%%/html/packages.html
-%%DOCSDIR%%/html/resources.html
-%%DOCSDIR%%/html/right.jpg
-%%DOCSDIR%%/html/up.jpg
+%%ALLDOCS%%%%DOCSDIR%%/html/NEWS.html
+%%ALLDOCS%%%%DOCSDIR%%/html/NEWS.2.html
+%%ALLDOCS%%%%DOCSDIR%%/html/R.css
+%%ALLDOCS%%%%DOCSDIR%%/html/SearchOn.html
+%%ALLDOCS%%%%DOCSDIR%%/html/Search.html
+%%ALLDOCS%%%%DOCSDIR%%/html/about.html
+%%ALLDOCS%%%%DOCSDIR%%/html/favicon.ico
+%%ALLDOCS%%%%DOCSDIR%%/html/index.html
+%%ALLDOCS%%%%DOCSDIR%%/html/left.jpg
+%%ALLDOCS%%%%DOCSDIR%%/html/logo.jpg
+%%ALLDOCS%%%%DOCSDIR%%/html/packages-head-utf8.html
+%%ALLDOCS%%%%DOCSDIR%%/html/packages.html
+%%ALLDOCS%%%%DOCSDIR%%/html/resources.html
+%%ALLDOCS%%%%DOCSDIR%%/html/right.jpg
+%%ALLDOCS%%%%DOCSDIR%%/html/up.jpg
 bin/R
 bin/Rscript
 lib/R/COPYING
@@ -116,13 +117,13 @@ lib/R/library/KernSmooth/NAMESPACE
 lib/R/library/KernSmooth/R/KernSmooth
 lib/R/library/KernSmooth/R/KernSmooth.rdb
 lib/R/library/KernSmooth/R/KernSmooth.rdx
-lib/R/library/KernSmooth/help/AnIndex
-lib/R/library/KernSmooth/help/KernSmooth.rdb
-lib/R/library/KernSmooth/help/KernSmooth.rdx
-lib/R/library/KernSmooth/help/aliases.rds
-lib/R/library/KernSmooth/help/paths.rds
-lib/R/library/KernSmooth/html/00Index.html
-lib/R/library/KernSmooth/html/R.css
+%%ALLDOCS%%lib/R/library/KernSmooth/help/AnIndex
+%%ALLDOCS%%lib/R/library/KernSmooth/help/KernSmooth.rdb
+%%ALLDOCS%%lib/R/library/KernSmooth/help/KernSmooth.rdx
+%%ALLDOCS%%lib/R/library/KernSmooth/help/aliases.rds
+%%ALLDOCS%%lib/R/library/KernSmooth/help/paths.rds
+%%ALLDOCS%%lib/R/library/KernSmooth/html/00Index.html
+%%ALLDOCS%%lib/R/library/KernSmooth/html/R.css
 lib/R/library/KernSmooth/libs/KernSmooth.so
 %%NLS%%lib/R/library/KernSmooth/po/de/LC_MESSAGES/R-KernSmooth.mo
 %%NLS%%lib/R/library/KernSmooth/po/en@quot/LC_MESSAGES/R-KernSmooth.mo
@@ -146,13 +147,13 @@ lib/R/library/MASS/R/MASS.rdx
 lib/R/library/MASS/data/Rdata.rdb
 lib/R/library/MASS/data/Rdata.rds
 lib/R/library/MASS/data/Rdata.rdx
-lib/R/library/MASS/help/AnIndex
-lib/R/library/MASS/help/MASS.rdb
-lib/R/library/MASS/help/MASS.rdx
-lib/R/library/MASS/help/aliases.rds
-lib/R/library/MASS/help/paths.rds
-lib/R/library/MASS/html/00Index.html
-lib/R/library/MASS/html/R.css
+%%ALLDOCS%%lib/R/library/MASS/help/AnIndex
+%%ALLDOCS%%lib/R/library/MASS/help/MASS.rdb
+%%ALLDOCS%%lib/R/library/MASS/help/MASS.rdx
+%%ALLDOCS%%lib/R/library/MASS/help/aliases.rds
+%%ALLDOCS%%lib/R/library/MASS/help/paths.rds
+%%ALLDOCS%%lib/R/library/MASS/html/00Index.html
+%%ALLDOCS%%lib/R/library/MASS/html/R.css
 lib/R/library/MASS/libs/MASS.so
 %%NLS%%lib/R/library/MASS/po/de/LC_MESSAGES/R-MASS.mo
 %%NLS%%lib/R/library/MASS/po/en@quot/LC_MESSAGES/R-MASS.mo
@@ -195,29 +196,29 @@ lib/R/library/Matrix/R/Matrix.rdx
 lib/R/library/Matrix/data/CAex.R
 lib/R/library/Matrix/data/KNex.R
 lib/R/library/Matrix/data/USCounties.R
-lib/R/library/Matrix/doc/Announce.txt
-lib/R/library/Matrix/doc/Comparisons.R
-lib/R/library/Matrix/doc/Comparisons.Rnw
-lib/R/library/Matrix/doc/Comparisons.pdf
-lib/R/library/Matrix/doc/Design-issues.R
-lib/R/library/Matrix/doc/Design-issues.Rnw
-lib/R/library/Matrix/doc/Design-issues.pdf
-lib/R/library/Matrix/doc/Intro2Matrix.R
-lib/R/library/Matrix/doc/Intro2Matrix.Rnw
-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/SuiteSparse/AMD.txt
-lib/R/library/Matrix/doc/SuiteSparse/CHOLMOD.txt
-lib/R/library/Matrix/doc/SuiteSparse/COLAMD.txt
-lib/R/library/Matrix/doc/SuiteSparse/SPQR.txt
-lib/R/library/Matrix/doc/SuiteSparse/SuiteSparse_config.txt
-lib/R/library/Matrix/doc/SuiteSparse/UserGuides.txt
-lib/R/library/Matrix/doc/index.html
-lib/R/library/Matrix/doc/sparseModels.R
-lib/R/library/Matrix/doc/sparseModels.Rnw
-lib/R/library/Matrix/doc/sparseModels.pdf
+%%ALLDOCS%%lib/R/library/Matrix/doc/Announce.txt
+%%ALLDOCS%%lib/R/library/Matrix/doc/Comparisons.R
+%%ALLDOCS%%lib/R/library/Matrix/doc/Comparisons.Rnw
+%%ALLDOCS%%lib/R/library/Matrix/doc/Comparisons.pdf
+%%ALLDOCS%%lib/R/library/Matrix/doc/Design-issues.R
+%%ALLDOCS%%lib/R/library/Matrix/doc/Design-issues.Rnw
+%%ALLDOCS%%lib/R/library/Matrix/doc/Design-issues.pdf
+%%ALLDOCS%%lib/R/library/Matrix/doc/Intro2Matrix.R
+%%ALLDOCS%%lib/R/library/Matrix/doc/Intro2Matrix.Rnw
+%%ALLDOCS%%lib/R/library/Matrix/doc/Intro2Matrix.pdf
+%%ALLDOCS%%lib/R/library/Matrix/doc/Introduction.R
+%%ALLDOCS%%lib/R/library/Matrix/doc/Introduction.Rnw
+%%ALLDOCS%%lib/R/library/Matrix/doc/Introduction.pdf
+%%ALLDOCS%%lib/R/library/Matrix/doc/SuiteSparse/AMD.txt
+%%ALLDOCS%%lib/R/library/Matrix/doc/SuiteSparse/CHOLMOD.txt
+%%ALLDOCS%%lib/R/library/Matrix/doc/SuiteSparse/COLAMD.txt
+%%ALLDOCS%%lib/R/library/Matrix/doc/SuiteSparse/SPQR.txt
+%%ALLDOCS%%lib/R/library/Matrix/doc/SuiteSparse/SuiteSparse_config.txt
+%%ALLDOCS%%lib/R/library/Matrix/doc/SuiteSparse/UserGuides.txt
+%%ALLDOCS%%lib/R/library/Matrix/doc/index.html
+%%ALLDOCS%%lib/R/library/Matrix/doc/sparseModels.R
+%%ALLDOCS%%lib/R/library/Matrix/doc/sparseModels.Rnw
+%%ALLDOCS%%lib/R/library/Matrix/doc/sparseModels.pdf
 lib/R/library/Matrix/external/CAex_slots.rda
 lib/R/library/Matrix/external/KNex_slots.rda
 lib/R/library/Matrix/external/USCounties_slots.rda
@@ -229,13 +230,13 @@ lib/R/library/Matrix/external/symW.rda
 lib/R/library/Matrix/external/test3comp.rda
 lib/R/library/Matrix/external/utm300.rua
 lib/R/library/Matrix/external/wrong.mtx
-lib/R/library/Matrix/help/AnIndex
-lib/R/library/Matrix/help/Matrix.rdb
-lib/R/library/Matrix/help/Matrix.rdx
-lib/R/library/Matrix/help/aliases.rds
-lib/R/library/Matrix/help/paths.rds
-lib/R/library/Matrix/html/00Index.html
-lib/R/library/Matrix/html/R.css
+%%ALLDOCS%%lib/R/library/Matrix/help/AnIndex
+%%ALLDOCS%%lib/R/library/Matrix/help/Matrix.rdb
+%%ALLDOCS%%lib/R/library/Matrix/help/Matrix.rdx
+%%ALLDOCS%%lib/R/library/Matrix/help/aliases.rds
+%%ALLDOCS%%lib/R/library/Matrix/help/paths.rds
+%%ALLDOCS%%lib/R/library/Matrix/html/00Index.html
+%%ALLDOCS%%lib/R/library/Matrix/html/R.css
 lib/R/library/Matrix/include/Matrix.h
 lib/R/library/Matrix/include/Matrix_stubs.c
 lib/R/library/Matrix/include/cholmod.h
@@ -268,13 +269,13 @@ lib/R/library/base/demo/error.catching.R
 lib/R/library/base/demo/is.things.R
 lib/R/library/base/demo/recursion.R
 lib/R/library/base/demo/scoping.R
-lib/R/library/base/help/AnIndex
-lib/R/library/base/help/aliases.rds
-lib/R/library/base/help/base.rdb
-lib/R/library/base/help/base.rdx
-lib/R/library/base/help/paths.rds
-lib/R/library/base/html/00Index.html
-lib/R/library/base/html/R.css
+%%ALLDOCS%%lib/R/library/base/help/AnIndex
+%%ALLDOCS%%lib/R/library/base/help/aliases.rds
+%%ALLDOCS%%lib/R/library/base/help/base.rdb
+%%ALLDOCS%%lib/R/library/base/help/base.rdx
+%%ALLDOCS%%lib/R/library/base/help/paths.rds
+%%ALLDOCS%%lib/R/library/base/html/00Index.html
+%%ALLDOCS%%lib/R/library/base/html/R.css
 lib/R/library/boot/CITATION
 lib/R/library/boot/DESCRIPTION
 lib/R/library/boot/INDEX
@@ -292,13 +293,13 @@ lib/R/library/boot/data/Rdata.rdb
 lib/R/library/boot/data/Rdata.rds
 lib/R/library/boot/data/Rdata.rdx
 lib/R/library/boot/bd.q
-lib/R/library/boot/help/AnIndex
-lib/R/library/boot/help/aliases.rds
-lib/R/library/boot/help/boot.rdb
-lib/R/library/boot/help/boot.rdx
-lib/R/library/boot/help/paths.rds
-lib/R/library/boot/html/00Index.html
-lib/R/library/boot/html/R.css
+%%ALLDOCS%%lib/R/library/boot/help/AnIndex
+%%ALLDOCS%%lib/R/library/boot/help/aliases.rds
+%%ALLDOCS%%lib/R/library/boot/help/boot.rdb
+%%ALLDOCS%%lib/R/library/boot/help/boot.rdx
+%%ALLDOCS%%lib/R/library/boot/help/paths.rds
+%%ALLDOCS%%lib/R/library/boot/html/00Index.html
+%%ALLDOCS%%lib/R/library/boot/html/R.css
 %%NLS%%lib/R/library/boot/po/de/LC_MESSAGES/R-boot.mo
 %%NLS%%lib/R/library/boot/po/en@quot/LC_MESSAGES/R-boot.mo
 %%NLS%%lib/R/library/boot/po/fr/LC_MESSAGES/R-boot.mo
@@ -318,13 +319,13 @@ lib/R/library/class/NEWS
 lib/R/library/class/R/class
 lib/R/library/class/R/class.rdb
 lib/R/library/class/R/class.rdx
-lib/R/library/class/help/AnIndex
-lib/R/library/class/help/aliases.rds
-lib/R/library/class/help/class.rdb
-lib/R/library/class/help/class.rdx
-lib/R/library/class/help/paths.rds
-lib/R/library/class/html/00Index.html
-lib/R/library/class/html/R.css
+%%ALLDOCS%%lib/R/library/class/help/AnIndex
+%%ALLDOCS%%lib/R/library/class/help/aliases.rds
+%%ALLDOCS%%lib/R/library/class/help/class.rdb
+%%ALLDOCS%%lib/R/library/class/help/class.rdx
+%%ALLDOCS%%lib/R/library/class/help/paths.rds
+%%ALLDOCS%%lib/R/library/class/html/00Index.html
+%%ALLDOCS%%lib/R/library/class/html/R.css
 lib/R/library/class/libs/class.so
 %%NLS%%lib/R/library/class/po/de/LC_MESSAGES/R-class.mo
 %%NLS%%lib/R/library/class/po/en@quot/LC_MESSAGES/R-class.mo
@@ -348,13 +349,13 @@ lib/R/library/cluster/R/cluster.rdx
 lib/R/library/cluster/data/Rdata.rdb
 lib/R/library/cluster/data/Rdata.rds
 lib/R/library/cluster/data/Rdata.rdx
-lib/R/library/cluster/help/AnIndex
-lib/R/library/cluster/help/aliases.rds
-lib/R/library/cluster/help/cluster.rdb
-lib/R/library/cluster/help/cluster.rdx
-lib/R/library/cluster/help/paths.rds
-lib/R/library/cluster/html/00Index.html
-lib/R/library/cluster/html/R.css
+%%ALLDOCS%%lib/R/library/cluster/help/AnIndex
+%%ALLDOCS%%lib/R/library/cluster/help/aliases.rds
+%%ALLDOCS%%lib/R/library/cluster/help/cluster.rdb
+%%ALLDOCS%%lib/R/library/cluster/help/cluster.rdx
+%%ALLDOCS%%lib/R/library/cluster/help/paths.rds
+%%ALLDOCS%%lib/R/library/cluster/html/00Index.html
+%%ALLDOCS%%lib/R/library/cluster/html/R.css
 lib/R/library/cluster/libs/cluster.so
 %%NLS%%lib/R/library/cluster/po/de/LC_MESSAGES/R-cluster.mo
 %%NLS%%lib/R/library/cluster/po/de/LC_MESSAGES/cluster.mo
@@ -375,13 +376,13 @@ lib/R/library/codetools/NAMESPACE
 lib/R/library/codetools/R/codetools
 lib/R/library/codetools/R/codetools.rdb
 lib/R/library/codetools/R/codetools.rdx
-lib/R/library/codetools/help/AnIndex
-lib/R/library/codetools/help/aliases.rds
-lib/R/library/codetools/help/codetools.rdb
-lib/R/library/codetools/help/codetools.rdx
-lib/R/library/codetools/help/paths.rds
-lib/R/library/codetools/html/00Index.html
-lib/R/library/codetools/html/R.css
+%%ALLDOCS%%lib/R/library/codetools/help/AnIndex
+%%ALLDOCS%%lib/R/library/codetools/help/aliases.rds
+%%ALLDOCS%%lib/R/library/codetools/help/codetools.rdb
+%%ALLDOCS%%lib/R/library/codetools/help/codetools.rdx
+%%ALLDOCS%%lib/R/library/codetools/help/paths.rds
+%%ALLDOCS%%lib/R/library/codetools/html/00Index.html
+%%ALLDOCS%%lib/R/library/codetools/html/R.css
 lib/R/library/compiler/DESCRIPTION
 lib/R/library/compiler/INDEX
 lib/R/library/compiler/Meta/Rd.rds
@@ -393,13 +394,13 @@ lib/R/library/compiler/NAMESPACE
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