6 files changed, 193 insertions, 50 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index 08c197661059..c4ec8faf04f8 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME?=	R
-PORTVERSION=	3.0.2
-PORTREVISION=	7
+PORTVERSION=	3.2.2
 CATEGORIES=	math lang
 MASTER_SITES=	http://cran.r-project.org/%SUBDIR%/ \
 		ftp://cran.r-project.org/pub/R/%SUBDIR%/ \
@@ -22,15 +21,13 @@ MASTER_SITES=	http://cran.r-project.org/%SUBDIR%/ \
 MASTER_SITE_SUBDIR=	src/base/R-${PORTVERSION:C|\..*||}
 DISTNAME=	R-${PORTVERSION}
 
-PATCH_SITES=		LOCAL/bf
-PATCHFILES=		R-patched-20131112-r64207.diff.bz2
-
 MAINTAINER=	bf@FreeBSD.org
-COMMENT?=	A language for statistical computing and graphics
+COMMENT?=	Language for statistical computing and graphics
 
 LICENSE=	GPLv2
 
-BUILD_DEPENDS=		${LOCALBASE}/bin/gsed:${PORTSDIR}/textproc/gsed
+BUILD_DEPENDS=		${LOCALBASE}/bin/gsed:${PORTSDIR}/textproc/gsed \
+			texi2dvi:${PORTSDIR}/print/texinfo
 
 CONFIGURE_ENV=		LIBR_LDFLAGS="${LDFLAGS}" OBJC="${CC}" \
 			SED="${LOCALBASE}/bin/gsed" \
@@ -51,7 +48,7 @@ PLIST_SUB=		RMATH_SOVERSION="${RMATH_SOVERSION}"
 USE_LDCONFIG=		yes
 .else # LIBRMATH_SLAVEPORT
 ALL_TARGET=		all
-INSTALL_TARGET=		install
+INSTALL_TARGET=		install-strip
 CONFIGURE_ARGS=		--enable-memory-profiling rdocdir=${DOCSDIR} \
 			--with-system-bzlib --with-system-zlib
 CONFIGURE_ENV+=		FCFLAGS="${FFLAGS}" \
@@ -70,7 +67,7 @@ OPTIONS_DEFAULT+=	ICU PCRE_PORT THREADS
 RUN_DEPENDS+=		${LOCALBASE}/bin/gsed:${PORTSDIR}/textproc/gsed
 USE_LDCONFIG=		${PREFIX}/lib/R/lib
 #now only used to build the R.1 manpage:
-USES+=			makeinfo perl5
+USES+=			perl5
 USE_PERL5=		build
 
 OPTIONS_DEFINE+=	GHOSTSCRIPT INFO_MANUALS JPEG LETTER_PAPER LIBR \
@@ -263,12 +260,14 @@ PLIST_SUB+=		X11="@comment "
 
 .if ${PORT_OPTIONS:MINFO_MANUALS} && ${PORT_OPTIONS:MDOCS}
 ALL_TARGET+=	info
+CONFIGURE_ENV+=	INSTALL_INFO="${LOCALBASE}/bin/install-info" \
+		MAKEINFO="${LOCALBASE}/bin/makeinfo"
 INFO=		R-FAQ R-admin R-data R-exts R-intro R-lang
 .endif
 
 .if ${PORT_OPTIONS:MPDF_MANUALS} && ${PORT_OPTIONS:MDOCS}
 USE_TEX=		texlive dvipsk kpathsea pdftex
-BUILD_DEPENDS +=	texi2dvi:${PORTSDIR}/print/texinfo
+#BUILD_DEPENDS +=	texi2dvi:${PORTSDIR}/print/texinfo
 ALL_TARGET+=		pdf
 CONFIGURE_ENV +=	INSTALL_INFO="${LOCALBASE}/bin/install-info" \
 			MAKEINFO="${LOCALBASE}/bin/makeinfo"
@@ -327,7 +326,7 @@ post-patch:
 	${TAR} -czf temptgz --exclude='*/po/*' @$$tarfile ; \
 	${MV} temptgz $$tarfile ; \
 	done)
-	@${REINPLACE_CMD} -e '/ls -d $$(srcdir)\/inst/d' \
+	@${REINPLACE_CMD} -e '/ls -d $$srcdir\/inst/d' \
 		${WRKSRC}/src/library/translations/Makefile.in
 .endif
 
@@ -350,7 +349,7 @@ do-build:
 
 do-install:
 	@${MKDIR} ${STAGEDIR}${PREFIX}/lib/R/lib
-	@${INSTALL_DATA} ${WRKSRC}/src/main/libR.a ${STAGEDIR}${PREFIX}/lib/R/lib
+	${INSTALL_DATA} ${WRKSRC}/src/main/libR.a ${STAGEDIR}${PREFIX}/lib/R/lib
 
 .else # LIBR_SLAVEPORT
 
@@ -382,9 +381,9 @@ post-install:
 .endif # LIBR_SLAVEPORT
 .else # !LIBRMATH_SLAVEPORT
 do-install:
-	@${INSTALL_DATA} ${WRKSRC}/src/include/Rmath.h ${STAGEDIR}${PREFIX}/include
-	@${INSTALL_DATA} ${BUILD_WRKSRC}/libRmath.a ${STAGEDIR}${PREFIX}/lib
-	@${INSTALL_LIB} ${BUILD_WRKSRC}/libRmath.so \
+	${INSTALL_DATA} ${WRKSRC}/src/include/Rmath.h ${STAGEDIR}${PREFIX}/include
+	${INSTALL_DATA} ${BUILD_WRKSRC}/libRmath.a ${STAGEDIR}${PREFIX}/lib
+	${INSTALL_LIB} ${BUILD_WRKSRC}/libRmath.so \
 	${STAGEDIR}${PREFIX}/lib/libRmath.so.${RMATH_SOVERSION}
 	@(cd ${STAGEDIR}${PREFIX}/lib; ${LN} -sf libRmath.so.${RMATH_SOVERSION} libRmath.so)
 
diff --git a/math/R/distinfo b/math/R/distinfo
index a6199e498f39..49560340f657 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,4 +1,2 @@
-SHA256 (R-3.0.2.tar.gz) = 956e05ad60447955049285420b5a48e0526aa4db676fd9eadb4bcfb7ccdc024b
-SIZE (R-3.0.2.tar.gz) = 25364181
-SHA256 (R-patched-20131112-r64207.diff.bz2) = 536243821d94f9328c3d35609fc5b0a6dc9c5f8c2a9bfa39b3d6fba4d9d5c60e
-SIZE (R-patched-20131112-r64207.diff.bz2) = 60325
+SHA256 (R-3.2.2.tar.gz) = 9c9152e74134b68b0f3a1c7083764adc1cb56fd8336bec003fd0ca550cd2461d
+SIZE (R-3.2.2.tar.gz) = 29772864
diff --git a/math/R/files/patch-configure b/math/R/files/patch-configure
index a2080bef1904..238406c79108 100644
--- a/math/R/files/patch-configure
+++ b/math/R/files/patch-configure
@@ -1,17 +1,108 @@
-# Recognize makeinfo from texinfo 6.0
-# Extra linker flags for threaded tk
---- configure.orig	2013-09-17 22:06:13 UTC
+--- configure.orig	2015-08-13 09:21:16 UTC
 +++ configure
-@@ -5181,7 +5181,7 @@ if ${r_cv_prog_makeinfo_v4+:} false; the
+@@ -20589,13 +20589,13 @@ if test "x$ac_cv_lib_mw__mwvalidcheckl" 
+   LIBM="-lmw"
+ fi
+ 
+-  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lm" >&5
+-$as_echo_n "checking for cos in -lm... " >&6; }
++  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lquadmath -lm" >&5
++$as_echo_n "checking for cos in -lquadmath -lm... " >&6; }
+ if ${ac_cv_lib_m_cos+:} false; then :
    $as_echo_n "(cached) " >&6
  else
-   makeinfo_version=`${MAKEINFO} --version | \
--  grep "^makeinfo" | sed 's/[^)]*) \(.*\)/\1/'`
-+  grep -E "^(makeinfo|texi2any)" | sed 's/[^)]*) \(.*\)/\1/'`
- makeinfo_version_maj=`echo ${makeinfo_version} | cut -f1 -d.`
- makeinfo_version_min=`echo ${makeinfo_version} | \
-   cut -f2 -d. | tr -dc '0123456789.' `
-@@ -32742,7 +32742,7 @@ fi
+   ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lm  $LIBS"
++LIBS="-lquadmath -lm  $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h.  */
+ 
+@@ -20626,18 +20626,18 @@ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_cos" >&5
+ $as_echo "$ac_cv_lib_m_cos" >&6; }
+ if test "x$ac_cv_lib_m_cos" = xyes; then :
+-  LIBM="$LIBM -lm"
++  LIBM="$LIBM -lquadmath -lm"
+ fi
+ 
+   ;;
+ *)
+-  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lm" >&5
+-$as_echo_n "checking for cos in -lm... " >&6; }
++  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lquadmath -lm" >&5
++$as_echo_n "checking for cos in -lquadmath -lm... " >&6; }
+ if ${ac_cv_lib_m_cos+:} false; then :
+   $as_echo_n "(cached) " >&6
+ else
+   ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lm  $LIBS"
++LIBS="-lquadmath -lm  $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h.  */
+ 
+@@ -20668,7 +20668,7 @@ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_cos" >&5
+ $as_echo "$ac_cv_lib_m_cos" >&6; }
+ if test "x$ac_cv_lib_m_cos" = xyes; then :
+-  LIBM="-lm"
++  LIBM="-lquadmath -lm"
+ fi
+ 
+   ;;
+@@ -20679,13 +20679,13 @@ esac
+ ## </NOTE>
+ ## AC_CHECK_LIBM computes LIBM but does not add to LIBS, hence we do
+ ## the following as well.
+-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for sin in -lm" >&5
+-$as_echo_n "checking for sin in -lm... " >&6; }
++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for sin in -lquadmath -lm" >&5
++$as_echo_n "checking for sin in -lquadmath -lm... " >&6; }
+ if ${ac_cv_lib_m_sin+:} false; then :
+   $as_echo_n "(cached) " >&6
+ else
+   ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lm  $LIBS"
++LIBS="-lquadmath -lm  $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h.  */
+ 
+@@ -20720,7 +20720,7 @@ if test "x$ac_cv_lib_m_sin" = xyes; then
+ #define HAVE_LIBM 1
+ _ACEOF
+ 
+-  LIBS="-lm $LIBS"
++  LIBS="-lquadmath -lm $LIBS"
+ 
+ fi
+ 
+@@ -26166,7 +26166,7 @@ fi
+ ## if nothing was obtained for SHLIB_CXXLDFLAGS.
+ ##
+ ## Note also that some systems (formerly AIX) do not allow for unresolved
+-## symbols at link time.  For such systems, we link against -lm (in case
++## symbols at link time.  For such systems, we link against -lquadmath -lm (in case
+ ## it exists) when building a shlib module via SHLIB_LIBADD.
+ 
+ main_ld="${CC}"
+@@ -28310,7 +28310,7 @@ if ${ac_cv_lib_rt_clock_gettime+:} false
+   $as_echo_n "(cached) " >&6
+ else
+   ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lrt  $LIBS"
++LIBS=" $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h.  */
+ 
+@@ -28353,7 +28353,7 @@ if test "x$ac_cv_lib_rt_clock_gettime" =
+ #define HAVE_LIBRT 1
+ _ACEOF
+ 
+-  LIBS="-lrt $LIBS"
++  LIBS="$LIBS"
+ 
+ fi
+ 
+@@ -33267,7 +33267,7 @@ fi
      ## Part 2.  Try finding the tk library.
      if test -n "${TK_CONFIG}"; then
        . ${TK_CONFIG}
diff --git a/math/R/files/patch-src__nmath__standalone__test.c b/math/R/files/patch-src__nmath__standalone__test.c
index c79bceebed0a..582d1cb24594 100644
--- a/math/R/files/patch-src__nmath__standalone__test.c
+++ b/math/R/files/patch-src__nmath__standalone__test.c
@@ -1,6 +1,6 @@
---- src/nmath/standalone/test.c.orig	2009-06-22 18:12:00.000000000 -0400
-+++ src/nmath/standalone/test.c	2009-06-22 18:12:34.000000000 -0400
-@@ -38,7 +38,7 @@
+--- src/nmath/standalone/test.c.orig	2012-04-15 22:05:35 UTC
++++ src/nmath/standalone/test.c
+@@ -38,7 +38,7 @@ main(int argc, char** argv)
      qnorm(0.7, 0.0, 1.0, 0, 0);
      printf("*** loaded '%s'\n", argv[0]);
      set_seed(123, 456);
diff --git a/math/R/files/patch-src_extra_tre_tre-internal.h b/math/R/files/patch-src_extra_tre_tre-internal.h
index b9d39324d772..36a8c997fe16 100644
--- a/math/R/files/patch-src_extra_tre_tre-internal.h
+++ b/math/R/files/patch-src_extra_tre_tre-internal.h
@@ -1,4 +1,4 @@
---- src/extra/tre/tre-internal.h.orig	2015-01-20 15:25:01 UTC
+--- src/extra/tre/tre-internal.h.orig	2014-06-13 22:15:07 UTC
 +++ src/extra/tre/tre-internal.h
 @@ -17,6 +17,7 @@
  #include <wctype.h>
diff --git a/math/R/pkg-plist b/math/R/pkg-plist
index 7752a07f1305..9b6f3c645871 100644
--- a/math/R/pkg-plist
+++ b/math/R/pkg-plist
@@ -8,8 +8,6 @@
 %%DOCSDIR%%/NEWS.rds
 %%DOCSDIR%%/RESOURCES
 %%DOCSDIR%%/THANKS
-bin/R
-bin/Rscript
 %%DOCSDIR%%/html/NEWS.html
 %%DOCSDIR%%/html/R.css
 %%DOCSDIR%%/html/SearchOn.html
@@ -25,12 +23,9 @@ bin/Rscript
 %%DOCSDIR%%/html/resources.html
 %%DOCSDIR%%/html/right.jpg
 %%DOCSDIR%%/html/up.jpg
+bin/R
+bin/Rscript
 lib/R/COPYING
-lib/R/NEWS
-lib/R/NEWS.0
-lib/R/NEWS.1
-lib/R/NEWS.2
-lib/R/NEWS.pdf
 lib/R/SVN-REVISION
 lib/R/bin/BATCH
 lib/R/bin/COMPILE
@@ -77,6 +72,7 @@ lib/R/include/R_ext/Error.h
 lib/R/include/R_ext/GetX11Image.h
 lib/R/include/R_ext/GraphicsDevice.h
 lib/R/include/R_ext/GraphicsEngine.h
+lib/R/include/R_ext/Itermacros.h
 lib/R/include/R_ext/Lapack.h
 lib/R/include/R_ext/Linpack.h
 lib/R/include/R_ext/MathThreads.h
@@ -87,6 +83,7 @@ lib/R/include/R_ext/PrtUtil.h
 lib/R/include/R_ext/QuartzDevice.h
 lib/R/include/R_ext/RS.h
 lib/R/include/R_ext/RStartup.h
+lib/R/include/R_ext/Rallocators.h
 lib/R/include/R_ext/Random.h
 lib/R/include/R_ext/Rdynload.h
 lib/R/include/R_ext/R-ftp-http.h
@@ -130,6 +127,7 @@ 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
+%%NLS%%lib/R/library/KernSmooth/po/fr/LC_MESSAGES/R-KernSmooth.mo
 %%NLS%%lib/R/library/KernSmooth/po/ko/LC_MESSAGES/R-KernSmooth.mo
 %%NLS%%lib/R/library/KernSmooth/po/pl/LC_MESSAGES/R-KernSmooth.mo
 lib/R/library/MASS/CITATION
@@ -182,6 +180,7 @@ lib/R/library/Matrix/Copyrights
 lib/R/library/Matrix/DESCRIPTION
 lib/R/library/Matrix/Doxyfile
 lib/R/library/Matrix/INDEX
+lib/R/library/Matrix/NEWS.Rd
 lib/R/library/Matrix/Meta/Rd.rds
 lib/R/library/Matrix/Meta/data.rds
 lib/R/library/Matrix/Meta/hsearch.rds
@@ -225,6 +224,7 @@ lib/R/library/Matrix/external/USCounties_slots.rda
 lib/R/library/Matrix/external/lund_a.mtx
 lib/R/library/Matrix/external/lund_a.rsa
 lib/R/library/Matrix/external/pores_1.mtx
+lib/R/library/Matrix/external/symA.rda
 lib/R/library/Matrix/external/symW.rda
 lib/R/library/Matrix/external/test3comp.rda
 lib/R/library/Matrix/external/utm300.rua
@@ -244,6 +244,9 @@ lib/R/library/Matrix/libs/Matrix.so
 %%NLS%%lib/R/library/Matrix/po/de/LC_MESSAGES/R-Matrix.mo
 %%NLS%%lib/R/library/Matrix/po/en@quot/LC_MESSAGES/Matrix.mo
 %%NLS%%lib/R/library/Matrix/po/en@quot/LC_MESSAGES/R-Matrix.mo
+%%NLS%%lib/R/library/Matrix/po/fr/LC_MESSAGES/Matrix.mo
+%%NLS%%lib/R/library/Matrix/po/fr/LC_MESSAGES/R-Matrix.mo
+%%NLS%%lib/R/library/Matrix/po/ko/LC_MESSAGES/R-Matrix.mo
 %%NLS%%lib/R/library/Matrix/po/pl/LC_MESSAGES/Matrix.mo
 %%NLS%%lib/R/library/Matrix/po/pl/LC_MESSAGES/R-Matrix.mo
 lib/R/library/Matrix/test-tools-1.R
@@ -288,6 +291,7 @@ lib/R/library/boot/R/boot.rdx
 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
@@ -337,6 +341,7 @@ lib/R/library/cluster/Meta/links.rds
 lib/R/library/cluster/Meta/nsInfo.rds
 lib/R/library/cluster/Meta/package.rds
 lib/R/library/cluster/NAMESPACE
+lib/R/library/cluster/NEWS.Rd
 lib/R/library/cluster/R/cluster
 lib/R/library/cluster/R/cluster.rdb
 lib/R/library/cluster/R/cluster.rdx
@@ -352,6 +357,11 @@ lib/R/library/cluster/html/00Index.html
 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
+%%NLS%%lib/R/library/cluster/po/en@quot/LC_MESSAGES/cluster.mo
+%%NLS%%lib/R/library/cluster/po/fr/LC_MESSAGES/R-cluster.mo
+%%NLS%%lib/R/library/cluster/po/ko/LC_MESSAGES/R-cluster.mo
+%%NLS%%lib/R/library/cluster/po/ko/LC_MESSAGES/cluster.mo
 %%NLS%%lib/R/library/cluster/po/en@quot/LC_MESSAGES/R-cluster.mo
 %%NLS%%lib/R/library/cluster/po/pl/LC_MESSAGES/R-cluster.mo
 lib/R/library/codetools/DESCRIPTION
@@ -453,6 +463,10 @@ lib/R/library/grDevices/NAMESPACE
 lib/R/library/grDevices/R/grDevices
 lib/R/library/grDevices/R/grDevices.rdb
 lib/R/library/grDevices/R/grDevices.rdx
+lib/R/library/grDevices/afm/ArialMT-Bold.afm.gz
+lib/R/library/grDevices/afm/ArialMT-BoldItalic.afm.gz
+lib/R/library/grDevices/afm/ArialMT-Italic.afm.gz
+lib/R/library/grDevices/afm/ArialMT.afm.gz
 lib/R/library/grDevices/afm/CM_boldx_10.afm.gz
 lib/R/library/grDevices/afm/CM_boldx_italic_10.afm.gz
 lib/R/library/grDevices/afm/CM_italic_10.afm.gz
@@ -608,6 +622,7 @@ lib/R/library/graphics/html/R.css
 lib/R/library/graphics/libs/graphics.so
 lib/R/library/grid/DESCRIPTION
 lib/R/library/grid/INDEX
+lib/R/library/grid/doc/DivByZero.txt
 lib/R/library/grid/Meta/Rd.rds
 lib/R/library/grid/Meta/hsearch.rds
 lib/R/library/grid/Meta/links.rds
@@ -699,9 +714,9 @@ lib/R/library/lattice/html/R.css
 lib/R/library/lattice/libs/lattice.so
 %%NLS%%lib/R/library/lattice/po/de/LC_MESSAGES/R-lattice.mo
 %%NLS%%lib/R/library/lattice/po/en@quot/LC_MESSAGES/R-lattice.mo
+%%NLS%%lib/R/library/lattice/po/pl/LC_MESSAGES/R-lattice.mo
 %%NLS%%lib/R/library/lattice/po/fr/LC_MESSAGES/R-lattice.mo
 %%NLS%%lib/R/library/lattice/po/ko/LC_MESSAGES/R-lattice.mo
-%%NLS%%lib/R/library/lattice/po/pl_PL/LC_MESSAGES/R-lattice.mo
 lib/R/library/methods/DESCRIPTION
 lib/R/library/methods/INDEX
 lib/R/library/methods/Meta/Rd.rds
@@ -744,6 +759,16 @@ lib/R/library/mgcv/help/paths.rds
 lib/R/library/mgcv/html/00Index.html
 lib/R/library/mgcv/html/R.css
 lib/R/library/mgcv/libs/mgcv.so
+%%NLS%%lib/R/library/mgcv/po/de/LC_MESSAGES/R-mgcv.mo
+%%NLS%%lib/R/library/mgcv/po/de/LC_MESSAGES/mgcv.mo
+%%NLS%%lib/R/library/mgcv/po/en@quot/LC_MESSAGES/R-mgcv.mo
+%%NLS%%lib/R/library/mgcv/po/en@quot/LC_MESSAGES/mgcv.mo
+%%NLS%%lib/R/library/mgcv/po/fr/LC_MESSAGES/R-mgcv.mo
+%%NLS%%lib/R/library/mgcv/po/fr/LC_MESSAGES/mgcv.mo
+%%NLS%%lib/R/library/mgcv/po/ko/LC_MESSAGES/R-mgcv.mo
+%%NLS%%lib/R/library/mgcv/po/ko/LC_MESSAGES/mgcv.mo
+%%NLS%%lib/R/library/mgcv/po/pl/LC_MESSAGES/R-mgcv.mo
+%%NLS%%lib/R/library/mgcv/po/pl/LC_MESSAGES/mgcv.mo
 lib/R/library/nlme/CITATION
 lib/R/library/nlme/DESCRIPTION
 lib/R/library/nlme/INDEX
@@ -905,6 +930,7 @@ lib/R/library/spatial/help/spatial.rdx
 lib/R/library/spatial/html/00Index.html
 lib/R/library/spatial/html/R.css
 lib/R/library/spatial/libs/spatial.so
+%%NLS%%lib/R/library/spatial/po/ko/LC_MESSAGES/R-spatial.mo
 %%NLS%%lib/R/library/spatial/po/de/LC_MESSAGES/R-spatial.mo
 %%NLS%%lib/R/library/spatial/po/en@quot/LC_MESSAGES/R-spatial.mo
 %%NLS%%lib/R/library/spatial/po/fr/LC_MESSAGES/R-spatial.mo
@@ -996,9 +1022,11 @@ lib/R/library/stats/help/stats.rdx
 lib/R/library/stats/html/00Index.html
 lib/R/library/stats/html/R.css
 lib/R/library/stats/libs/stats.so
+lib/R/library/survival/COPYRIGHTS
 lib/R/library/survival/CITATION
 lib/R/library/survival/DESCRIPTION
 lib/R/library/survival/INDEX
+lib/R/library/survival/data/datalist
 lib/R/library/survival/Meta/Rd.rds
 lib/R/library/survival/Meta/data.rds
 lib/R/library/survival/Meta/hsearch.rds
@@ -1015,6 +1043,18 @@ 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/adjcurve.R
+lib/R/library/survival/doc/adjcurve.Rnw
+lib/R/library/survival/doc/adjcurve.pdf
+lib/R/library/survival/doc/compete.R
+lib/R/library/survival/doc/compete.Rnw
+lib/R/library/survival/doc/compete.pdf
+lib/R/library/survival/doc/splines.R
+lib/R/library/survival/doc/splines.Rnw
+lib/R/library/survival/doc/splines.pdf
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 lib/R/library/survival/doc/timedep.R
 lib/R/library/survival/doc/timedep.Rnw
 lib/R/library/survival/doc/timedep.pdf
@@ -1071,6 +1111,8 @@ lib/R/library/tools/Meta/links.rds
 lib/R/library/tools/Meta/nsInfo.rds
 lib/R/library/tools/Meta/package.rds
 lib/R/library/tools/NAMESPACE
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 lib/R/library/tools/R/tools
 lib/R/library/tools/R/tools.rdb
 lib/R/library/tools/R/tools.rdx
@@ -1131,6 +1173,7 @@ lib/R/library/translations/DESCRIPTION
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 %%NLS%%lib/R/library/translations/de/LC_MESSAGES/tcltk.mo
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 %%NLS%%lib/R/library/translations/en@quot/LC_MESSAGES/R-base.mo
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@@ -1394,12 +1437,12 @@ lib/R/library/utils/misc/exDIF.dif
 %%X11%%lib/R/modules/R_de.so
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 lib/R/modules/lapack.so
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 lib/R/share/R/examples-footer.R
 lib/R/share/R/examples-header.R
 lib/R/share/R/nspackloader.R
 lib/R/share/R/tests-startup.R
+lib/R/share/Rd/macros/system.Rd
 lib/R/share/dictionaries/en_stats.rds
 lib/R/share/encodings/Adobe-glyphlist
 lib/R/share/encodings/character-sets
@@ -1441,18 +1484,30 @@ lib/R/share/texmf/tex/latex/ts1aett.fd
 man/man1/R.1.gz
 man/man1/Rscript.1.gz
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-%%DOCSDIR%%/manual/R-lang.html
 %%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-lang.pdf
 %%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/fullrefman.pdf
+%%PORTDOCS%%%%DOCSDIR%%/BioC_mirrors.csv
+%%PORTDOCS%%%%DOCSDIR%%/NEWS
+%%PORTDOCS%%%%DOCSDIR%%/NEWS.0
+%%PORTDOCS%%%%DOCSDIR%%/NEWS.1
+%%PORTDOCS%%%%DOCSDIR%%/NEWS.2
+%%PORTDOCS%%%%DOCSDIR%%/NEWS.pdf
+%%PORTDOCS%%%%DOCSDIR%%/manual/images/QQ.png
+%%PORTDOCS%%%%DOCSDIR%%/manual/images/ecdf.png
+%%PORTDOCS%%%%DOCSDIR%%/manual/images/fig11.png
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+%%PORTDOCS%%%%DOCSDIR%%/manual/images/hist.png
+%%PORTDOCS%%%%DOCSDIR%%/manual/images/ice.png
+%%PORTDOCS%%%%DOCSDIR%%/manual/R-FAQ.html
+%%PORTDOCS%%%%DOCSDIR%%/manual/R-admin.html
+%%PORTDOCS%%%%DOCSDIR%%/manual/R-data.html
+%%PORTDOCS%%%%DOCSDIR%%/manual/R-exts.html
+%%PORTDOCS%%%%DOCSDIR%%/manual/R-intro.html
+%%PORTDOCS%%%%DOCSDIR%%/manual/R-ints.html
+%%PORTDOCS%%%%DOCSDIR%%/manual/R-lang.html