[Midnightbsd-cvs] mports [18827] trunk/math/R: R 3.0.2
laffer1 at midnightbsd.org
laffer1 at midnightbsd.org
Fri May 8 23:16:06 EDT 2015
Revision: 18827
http://svnweb.midnightbsd.org/mports/?rev=18827
Author: laffer1
Date: 2015-05-08 23:16:06 -0400 (Fri, 08 May 2015)
Log Message:
-----------
R 3.0.2
Modified Paths:
--------------
trunk/math/R/Makefile
trunk/math/R/distinfo
trunk/math/R/pkg-plist
Removed Paths:
-------------
trunk/math/R/files/patch-20130526
Modified: trunk/math/R/Makefile
===================================================================
--- trunk/math/R/Makefile 2015-05-09 03:12:24 UTC (rev 18826)
+++ trunk/math/R/Makefile 2015-05-09 03:16:06 UTC (rev 18827)
@@ -1,7 +1,9 @@
-# $MidnightBSD$
+# Created by: Maurice Castro <maurice at serc.rmit.edu.au>
+# $FreeBSD: head/math/R/Makefile 378945 2015-02-13 21:41:22Z sbruno $
PORTNAME?= R
-PORTVERSION= 3.0.1
+PORTVERSION= 3.0.2
+PORTREVISION= 3
CATEGORIES= math lang
MASTER_SITES= http://cran.r-project.org/%SUBDIR%/ \
ftp://cran.r-project.org/pub/R/%SUBDIR%/ \
@@ -20,16 +22,22 @@
MASTER_SITE_SUBDIR= src/base/R-${PORTVERSION:C|\..*||}
DISTNAME= R-${PORTVERSION}
+PATCH_SITES= ${MASTER_SITE_LOCAL}
+PATCH_SITE_SUBDIR= bf
+PATCHFILES= R-patched-20131112-r64207.diff.bz2
+
MAINTAINER= ports at MidnightBSD.org
COMMENT?= A language for statistical computing and graphics
+
LICENSE= gpl2
BUILD_DEPENDS= ${LOCALBASE}/bin/gsed:${PORTSDIR}/textproc/gsed
-CONFIGURE_ENV= SED="${LOCALBASE}/bin/gsed" \
+CONFIGURE_ENV= LIBR_LDFLAGS="${LDFLAGS}" OBJC="${CC}" \
+ SED="${LOCALBASE}/bin/gsed" \
ac_cv_have_decl_powl=yes ac_cv_have_decl_log1pl=yes
-OPTIONS_DEFINE= MISSING
+OPTIONS_DEFINE= MISSING DOCS
MISSING_DESC= use libmissing rather than libquadmath
@@ -44,11 +52,10 @@
USE_LDCONFIG= yes
.else # LIBRMATH_SLAVEPORT
ALL_TARGET= all
-INSTALL_TARGET = install
-CONFIGURE_ARGS = --enable-memory-profiling rdocdir=${DOCSDIR} \
+INSTALL_TARGET= install
+CONFIGURE_ARGS= --enable-memory-profiling rdocdir=${DOCSDIR} \
--with-system-bzlib --with-system-zlib
CONFIGURE_ENV+= FCFLAGS="${FFLAGS}" \
- INSTALL_DATA="${INSTALL} ${COPY} ${_SHROWNGRP} -m 644" \
R_LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}" TAR="${TAR}"
CPPFLAGS+= -I${LOCALBASE}/include
LDFLAGS+= -L${LOCALBASE}/lib
@@ -57,7 +64,7 @@
ATLAS_DESC= Use ATLAS instead of BLAS/LAPACK
ICU_DESC= Use ICU for collation in multibyte locales
-PCRE_PORT_DESC = Use devel/pcre instead of the bundled PCRE
+PCRE_PORT_DESC= Use devel/pcre instead of the bundled PCRE
OPTIONS_DEFAULT+= ICU PCRE_PORT THREADS
.if !defined(LIBR_SLAVEPORT)
@@ -64,10 +71,9 @@
RUN_DEPENDS+= ${LOCALBASE}/bin/gsed:${PORTSDIR}/textproc/gsed
USE_LDCONFIG= ${PREFIX}/lib/R/lib
#now only used to build the R.1 manpage:
-USE_PERL5_BUILD= yes
+USES+= makeinfo perl5
+USE_PERL5= build
-MAN1= R.1 Rscript.1
-
OPTIONS_DEFINE+= GHOSTSCRIPT INFO_MANUALS JPEG LETTER_PAPER LIBR \
PANGOCAIRO PDF_MANUALS PNG TCLTK TIFF X11
@@ -85,6 +91,10 @@
OPTIONS_DEFAULT+= GHOSTSCRIPT INFO_MANUALS JPEG LIBR PANGOCAIRO PNG \
TCLTK TIFF X11
+OPTIONS_DEFAULT_armv6+= MISSING
+OPTIONS_DEFAULT_powerpc+= MISSING
+OPTIONS_DEFAULT_powerpc64+= MISSING
+
.endif # !LIBR_SLAVEPORT
PLIST_SUB= R_SOVERSION="${R_SOVERSION}" \
RBLAS_SOVERSION="${RBLAS_SOVERSION}" \
@@ -98,36 +108,36 @@
RBLAS_SOVERSION= 2
RLAPACK_SOVERSION= 4
RMATH_SOVERSION= 0
-USE_FORTRAN= yes
+USES+= fortran
+USE_GCC= yes
.include <bsd.mport.options.mk>
-.if ${ARCH} == "sparc64"
-PICFLAG?= -fPIC
-.else
PICFLAG?= -fpic
-.endif
.for flag in LD CXXLD
CONFIGURE_ENV += SHLIB_${flag}FLAGS="${PICFLAG}"
.endfor
.if ${PORT_OPTIONS:MMISSING}
-LIB_DEPENDS+= missing:${PORTSDIR}/math/libmissing
-LIBM= -L${LOCALBASE}/lib -lmissing
+.for _f in acos asin atan cos cosh exp log pow sin sinh tan tanh
+CONFIGURE_ENV+= ac_cv_have_decl_c${_f}=yes
+.endfor
+LIB_DEPENDS+= libmissing.so:${PORTSDIR}/math/libmissing
+LIBM= -L${LOCALBASE}/lib -lmissing -lm
LIBMH= "missing_math.h"
.if defined(LIBRMATH_SLAVEPORT)
CPPFLAGS+= -I${LOCALBASE}/include
.endif
.else
-LIBM= -lquadmath
+LIBM= -lquadmath -lm
LIBMH= <quadmath.h>
.endif
.if !defined(LIBRMATH_SLAVEPORT)
.if ${PORT_OPTIONS:MATLAS}
-LIB_DEPENDS+= atlas:${PORTSDIR}/math/atlas
-BLAS?= -lf77blas
-LAPACK?= -lalapack -lcblas
+LIB_DEPENDS+= libatlas.so:${PORTSDIR}/math/atlas
+BLAS?= ${LIBM} -lf77blas
+LAPACK?= ${LIBM} -lalapack -lcblas
.else
BLAS?= no
LAPACK?= no
@@ -140,7 +150,7 @@
.endif
.if ${PORT_OPTIONS:MICU}
-LIB_DEPENDS+= icui18n:${PORTSDIR}/devel/icu
+LIB_DEPENDS+= libicui18n.so:${PORTSDIR}/devel/icu
CONFIGURE_ARGS+= --with-ICU
.else
CONFIGURE_ARGS+= --without-ICU
@@ -155,7 +165,7 @@
.endif
.if ${PORT_OPTIONS:MPCRE_PORT}
-LIB_DEPENDS+= pcre:${PORTSDIR}/devel/pcre
+LIB_DEPENDS+= libpcre.so:${PORTSDIR}/devel/pcre
CONFIGURE_ARGS+= --with-system-pcre
.else
CONFIGURE_ARGS+= --without-system-pcre
@@ -170,6 +180,7 @@
.if defined(LIBR_SLAVEPORT)
CONFIGURE_ARGS+= --disable-BLAS-shlib --without-pic --without-x
+USES+= readline
.else # LIBR_SLAVEPORT
@@ -178,7 +189,7 @@
.endif
.if ${PORT_OPTIONS:MJPEG}
-LIB_DEPENDS+= jpeg:${PORTSDIR}/graphics/jpeg
+LIB_DEPENDS+= libjpeg.so:${PORTSDIR}/graphics/jpeg
CONFIGURE_ARGS+= --with-jpeglib
.else
CONFIGURE_ARGS+= --without-jpeglib
@@ -196,6 +207,7 @@
.endif
.if ${PORT_OPTIONS:MPANGOCAIRO}
+USES+= pkgconfig
USE_GNOME+= pango
PLIST_SUB+= PANGOCAIRO=""
.else
@@ -204,7 +216,7 @@
.endif
.if ${PORT_OPTIONS:MPNG}
-LIB_DEPENDS+= png15:${PORTSDIR}/graphics/png
+LIB_DEPENDS+= libpng.so:${PORTSDIR}/graphics/png
CONFIGURE_ARGS+= --with-libpng
.else
CONFIGURE_ARGS+= --without-libpng
@@ -211,7 +223,7 @@
.endif
.if ${PORT_OPTIONS:MTCLTK}
-USE_TK = 84+
+USE_TK= 84+
CONFIGURE_ARGS+= --with-tcltk \
--with-tcl-config=${TCL_LIBDIR}/tclConfig.sh \
--with-tk-config=${TK_LIBDIR}/tkConfig.sh
@@ -222,7 +234,7 @@
.endif
.if ${PORT_OPTIONS:MTIFF}
-LIB_DEPENDS+= tiff:${PORTSDIR}/graphics/tiff
+LIB_DEPENDS+= libtiff.so:${PORTSDIR}/graphics/tiff
CONFIGURE_ARGS+= --with-libtiff
.else
CONFIGURE_ARGS+= --without-libtiff
@@ -243,9 +255,7 @@
.endif
.if ${PORT_OPTIONS:MPDF_MANUALS} && ${PORT_OPTIONS:MDOCS}
-BROKEN= The PDF_MANUALS option cannot be used, because it\
- requires broken components of texlive
-USE_TEX= texlive pdftex:build
+USE_TEX= texlive dvipsk kpathsea pdftex
BUILD_DEPENDS += texi2dvi:${PORTSDIR}/print/texinfo
ALL_TARGET+= pdf
CONFIGURE_ENV += INSTALL_INFO="${LOCALBASE}/bin/install-info" \
@@ -253,6 +263,9 @@
INSTALL_TARGET+= install-pdf
PLIST_SUB+= PDF_MANUAL=""
.else
+.for _b in KPSEWHICH MAKEINDEX PDFLATEX PDFTEX TEX TEXI2DVI
+CONFIGURE_ENV+= ac_cv_path_${_b}=""
+.endfor
PLIST_SUB+= PDF_MANUAL="@comment "
.endif
.endif # LIBR_SLAVEPORT
@@ -259,33 +272,45 @@
.endif # !LIBRMATH_SLAVEPORT
post-patch:
+ @${REINPLACE_CMD} -e '\|LIBS=|s|-lrt ||' \
+ -e '\|-lm[". ]|s|-lm|${LIBM}|' \
+ ${WRKSRC}/configure
.if !${PORT_OPTIONS:MMISSING}
.if ${OSVERSION} < 1000016
@${REINPLACE_CMD} -e 's/# define EXP expl/# define EXP(x) (long double)expq((__float128)(x))/' \
${WRKSRC}/src/nmath/pnchisq.c
.endif
+.if ${OSVERSION} < 1000034
@${REINPLACE_CMD} -Ee 's/(log)(1p)?l\(/(long double)\1\2q((__float128)/' \
${WRKSRC}/src/nmath/dnbeta.c \
${WRKSRC}/src/nmath/pnbeta.c
+.endif
@${REINPLACE_CMD} -Ee 's/powl\((.*)(long double)/(long double)powq((__float128)\1__float128/' \
${WRKSRC}/src/main/format.c
+.else
+.if ${OSVERSION} > 1000052 && \
+(${ARCH} == amd64 || ${ARCH} == i386 || ${ARCH} == ia64 || ${ARCH} == pc98 || ${ARCH} == sparc64)
+ @${REINPLACE_CMD} -e '\|^FLIBS="$$ac_cv_f77_libs"|s|"|&${LIBM} |' \
+ ${WRKSRC}/configure
.endif
@${REINPLACE_CMD} -e \
- '\|#include <math.h>|{x;s|^.*$$|#include ${LIBMH}|;H;x;}' \
- ${WRKSRC}/src/nmath/nmath.h
- @${REINPLACE_CMD} -e '\|LIBS=|s|-lrt ||' \
- -e '\|-lm[". ]|s|-lm|${LIBM}|' \
- ${WRKSRC}/configure
+ '\|#[[:blank:]]*include[[:blank:]]*<complex.h>|{x;s|^.*$$|#include "missing_complex.h"|;H;x;}' \
+ ${WRKSRC}/src/main/complex.c
+.endif
+ @${REINPLACE_CMD} -e \
+ '\|#[[:blank:]]*include[[:blank:]]*<math.h>|{x;s|^.*$$|#include ${LIBMH}|;H;x;}' \
+ ${WRKSRC}/src/nmath/nmath.h \
+ ${WRKSRC}/src/include/Rmath.h0.in
@${REINPLACE_CMD} -e 's|(libdir)/pkgconfig|(prefix)/libdata/pkgconfig|g' \
${WRKSRC}/src/nmath/standalone/Makefile.in \
${WRKSRC}/src/unix/Makefile.in
@${REINPLACE_CMD} -e "s|-lpthread|${PTHREAD_LIBS}|g" \
${WRKSRC}/configure \
- ${WRKSRC}/src/scripts/javareconf
+ ${WRKSRC}/src/scripts/javareconf.in
@${REINPLACE_CMD} -e "s|/usr/local|${LOCALBASE}|g" \
${WRKSRC}/configure \
${WRKSRC}/src/library/profile/Rprofile.unix \
- ${WRKSRC}/src/scripts/javareconf
+ ${WRKSRC}/src/scripts/javareconf.in
.if !defined(LIBRMATH_SLAVEPORT)
.if !${PORT_OPTIONS:MNLS}
@(cd ${WRKSRC}/src/library/Recommended; \
@@ -315,8 +340,8 @@
${MAKE_ARGS} Makefile Makedeps libR.a)
do-install:
- @${MKDIR} ${PREFIX}/lib/R/lib
- @${INSTALL_DATA} ${WRKSRC}/src/main/libR.a ${PREFIX}/lib/R/lib
+ @${MKDIR} ${STAGEDIR}${PREFIX}/lib/R/lib
+ @${INSTALL_LIB} ${WRKSRC}/src/main/libR.a ${STAGEDIR}${PREFIX}/lib/R/lib
.else # LIBR_SLAVEPORT
@@ -335,13 +360,13 @@
post-install:
.for L in R Rblas Rlapack
- @(cd ${PREFIX}/lib/R/lib; if [ -f lib${L}.so ] ; then \
- ${LN} -sf lib${L}.so lib${L}.so.${${L:U}_SOVERSION} ; fi)
+ @(cd ${STAGEDIR}${PREFIX}/lib/R/lib; if [ -f lib${L}.so ] ; then \
+ ${LN} -sf lib${L}.so lib${L}.so.${${L:tu}_SOVERSION} ; fi)
.endfor
.if ${PORT_OPTIONS:MINFO_MANUALS} && ${PORT_OPTIONS:MDOCS}
@(cd ${WRKSRC}/doc/manual; \
for infofile in ${INFO}; do \
- ${INSTALL_DATA} $${infofile}.info* ${PREFIX}/${INFO_PATH}/; \
+ ${INSTALL_DATA} $${infofile}.info* ${STAGEDIR}${PREFIX}/${INFO_PATH}/; \
done)
.endif
@@ -348,12 +373,11 @@
.endif # LIBR_SLAVEPORT
.else # !LIBRMATH_SLAVEPORT
do-install:
- @${INSTALL_DATA} ${WRKSRC}/src/include/Rmath.h ${PREFIX}/include
- @${INSTALL_DATA} ${BUILD_WRKSRC}/libRmath.a ${PREFIX}/lib
- @${STRIP_CMD} ${BUILD_WRKSRC}/libRmath.so
- @${INSTALL_DATA} ${BUILD_WRKSRC}/libRmath.so \
- ${PREFIX}/lib/libRmath.so.${RMATH_SOVERSION}
- @(cd ${PREFIX}/lib; ${LN} -sf libRmath.so.${RMATH_SOVERSION} 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)
check regression-test test: build
@(cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} LANGUAGE=en \
Modified: trunk/math/R/distinfo
===================================================================
--- trunk/math/R/distinfo 2015-05-09 03:12:24 UTC (rev 18826)
+++ trunk/math/R/distinfo 2015-05-09 03:16:06 UTC (rev 18827)
@@ -1,2 +1,4 @@
-SHA256 (R-3.0.1.tar.gz) = af90488af3141103b211dc81b6f17d1f0faf4f17684c579a32dfeb25d0d87134
-SIZE (R-3.0.1.tar.gz) = 25508280
+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
Deleted: trunk/math/R/files/patch-20130526
===================================================================
--- trunk/math/R/files/patch-20130526 2015-05-09 03:12:24 UTC (rev 18826)
+++ trunk/math/R/files/patch-20130526 2015-05-09 03:16:06 UTC (rev 18827)
@@ -1,2831 +0,0 @@
-diff -ruN R-3.0.1/NEWS R-patched/NEWS
---- NEWS 2013-05-16 03:05:47.000000000 -0400
-+++ NEWS 2013-05-26 18:10:19.000000000 -0400
-@@ -1,5 +1,44 @@
- R News
-
-+CHANGES IN R 3.0.1 patched:
-+
-+ NEW FEATURES:
-+
-+ o The macros used for the texinfo manuals have been changed to work
-+ better with the incompatible changes made in texinfo 5.x.
-+
-+ o The example() and tools::Rd2ex() functions now have parameters to
-+ allow them to ignore \dontrun markup in examples. (Suggested by
-+ Peter Solymos.)
-+
-+ C-LEVEL FACILITIES:
-+
-+ o Rdefines.h has been tweaked so it can be included in C++ code
-+ with R_exts/Boolean.h (which is included by R.h). Note though
-+ that Rdefines.h is not kept up-to-date, and Rinternals.h is
-+ preferred for new code.
-+
-+ BUG FIXES:
-+
-+ o help.request() could not determine the current version of R on
-+ CRAN. (PR#15241)
-+
-+ o On Windows, file.info() failed on root directories unless the
-+ path was terminated with an explicit ".". (PR#15302)
-+
-+ o The regmatches<-() replacement function mishandled results coming
-+ from regexpr(). (PR#15311)
-+
-+ o Documentation for setClass and representation still suggested the
-+ deprecated argument representation=. (PR#15312)
-+
-+ o R CMD config failed in an installed build of R 3.0.1 (only) when
-+ a sub-architecture was used. (Reported by Berwin Turlach.)
-+
-+ o On Windows, the installer modified the etc/Rconsole and
-+ etc/Rprofile.site files even when default options were chosen.
-+ (Reported by Tal Galili.)
-+
- CHANGES IN R 3.0.1:
-
- NEW FEATURES:
-Files R-3.0.1/NEWS.pdf and R-patched/NEWS.pdf differ
-diff -ruN R-3.0.1/SVN-REVISION R-patched/SVN-REVISION
---- SVN-REVISION 2013-05-16 03:01:22.000000000 -0400
-+++ SVN-REVISION 2013-05-26 18:06:20.000000000 -0400
-@@ -1,2 +1,2 @@
--Revision: 62743
--Last Changed Date: 2013-05-16
-+Revision: 62815
-+Last Changed Date: 2013-05-26
-diff -ruN R-3.0.1/VERSION R-patched/VERSION
---- VERSION 2013-05-16 03:00:06.000000000 -0400
-+++ VERSION 2013-05-16 03:11:45.000000000 -0400
-@@ -1 +1 @@
--3.0.1
-+3.0.1 Patched
-diff -ruN R-3.0.1/doc/CRAN_mirrors.csv R-patched/doc/CRAN_mirrors.csv
---- doc/CRAN_mirrors.csv 2013-04-18 18:05:05.000000000 -0400
-+++ doc/CRAN_mirrors.csv 2013-05-24 18:05:06.000000000 -0400
-@@ -32,7 +32,6 @@
- "France (Paris 2)",France,Paris,http://cran.univ-paris1.fr/,"Universite Paris 1 Pantheon-Sorbonne","pierre.latouche # univ-paris1.fr",1,fr
- "Germany (Berlin)",Germany,Berlin,http://mirrors.softliste.de/cran/,"Softliste.de, Berlin","docko # docko.sk",1,de
- "Germany (Bonn)",Germany,Bonn,http://cran.r-mirror.de/,"Stefan Drees, Bonn","stefan # drees.name",1,de
--"Germany (Falkenstein)",Germany,Falkenstein,http://mirror.layerjet.com/cran,layerjet.com,"Elton Chung <elton # layerjet.com>",1,de
- "Germany (Goettingen)",Germany,Goettingen,http://ftp5.gwdg.de/pub/misc/cran/,"GWDG Goettingen","Eberhard Moenkeberg <emoenke # gwdg.de>",1,de
- Greece,Greece,Crete,http://cran.cc.uoc.gr/,"University of Crete","mirrors # Cc.uoc.gr",1,gr
- Hungary,Hungary,Budapest,http://cran.rapporter.net/,"Rapporter.net, Budapest","Daróczi Gergely <gergely # snowl.net>",1,hu
-@@ -48,7 +47,6 @@
- "Japan (Tokyo)",Japan,Tokyo,http://cran.ism.ac.jp/,"Institute of Statistical Mathematics, Tokyo","Junji Nakano <nakanoj # ism.ac.jp>",1,jp
- "Korea (Seoul 1)",Korea,Seoul,http://cran.nexr.com/,"NexR Corporation, Seoul","mining # nexr.com",1,kr
- "Korea (Seoul 2)",Korea,Seoul,http://biostat.cau.ac.kr/CRAN/,"Chung-Ang University, Seoul","Sunghow # gmail.com",1,kr
--Latvia,Latvia,Riga,http://mirrors.webhostinggeeks.com/cran/,Webhostinggeeks,"whg.igp # gmail.com",1,lv
- "Mexico (Mexico City)",Mexico,"Mexico City",http://cran.itam.mx/,"Instituto Tecnologico Autonomo de Mexico","Ernesto Barrios <ebarrios # Itam.mx>",1,mx
- "Mexico (Texcoco)",Mexico,Texcoco,http://www.est.colpos.mx/R-mirror/,"Colegio de Postgraduados, Texcoco","perpdgo # gmail.com",1,mx
- "Netherlands (Amsterdam)",Netherlands,Amsterdam,http://cran.xl-mirror.nl/,"XL-Data, Amsterdam","werner # xl-mirror.nl",1,nl
-@@ -57,6 +55,7 @@
- Norway,Norway,Bergen,http://cran.uib.no/,"University of Bergen","sundrift # It.uib.no",1,no
- Philippines,Philippines,"Quezon City",http://cran.stat.upd.edu.ph/,"University of the Philippines and PREGINET","edward.p.santos # Up.edu.ph",1,ph
- Poland,Poland,Wroclaw,http://r.meteo.uni.wroc.pl/,"University of Wroclaw","Paweł Netzel <netzel # meteo.uni.wroc.pl>",1,pl
-+Portugal,Portugal,Porto,http://cran.dcc.fc.up.pt/,"University of Porto","labcc # labcc.dcc.fc.up.pt",1,pt
- Russia,Russia,Moscow,http://cran.gis-lab.info/,GIS-Lab.info,"sim # gis-lab.info",1,ru
- Singapore,Singapore,Singapore,http://cran.stat.nus.edu.sg/,"National University of Singapore","Zhang Rong <ccezr # nus.edu.sg>",1,sg
- Slovakia,Slovakia,Bratislava,http://cran.fyxm.net/,"FYXM.net, Bratislava","docko # docko.sk",1,sk
-@@ -74,7 +73,7 @@
- "UK (St Andrews)",UK,"St Andrews",http://star-www.st-andrews.ac.uk/cran/,"St Andrews University","Lee Kelvin <lsk9 # St-andrews.ac.uk>",1,uk
- "USA (CA 1)",USA,Berkeley,http://cran.cnr.Berkeley.edu,"University of California, Berkeley, CA","casterln # nature.berkeley.edu",1,us
- "USA (CA 2)",USA,"Los Angeles",http://cran.stat.ucla.edu/,"University of California, Los Angeles, CA","Jose Hales-Garcia <jose # stat.ucla.edu>",1,us
--"USA (IA)",USA,Ames,http://streaming.stat.iastate.edu/CRAN/,"Iowa State University, Ames, IA","Ted Peterson <statit # iastate.edu>",1,us
-+"USA (IA)",USA,Ames,http://streaming.stat.iastate.edu/CRAN/,"Iowa State University, Ames, IA","statit # iastate.edu",1,us
- "USA (IN)",USA,Bloomington,http://ftp.ussg.iu.edu/CRAN/,"Indiana University","rtadmin # indiana.edu",1,us
- "USA (KS)",USA,Lawrence,http://rweb.quant.ku.edu/cran/,"University of Kansas, Lawrence, KS","Paul Johnson <pauljohn # ku.edu>",1,us
- "USA (MD)",USA,Bethesda,http://watson.nci.nih.gov/cran_mirror/,"National Cancer Institute, Bethesda, MD","Sean Davis <sdavis2 # mail.nih.gov>",1,us
-diff -ruN R-3.0.1/doc/NEWS.Rd R-patched/doc/NEWS.Rd
---- doc/NEWS.Rd 2013-05-11 18:05:03.000000000 -0400
-+++ doc/NEWS.Rd 2013-05-25 18:05:04.000000000 -0400
-@@ -7,6 +7,53 @@
- \title{ R News}
- \encoding{UTF-8}
-
-+\section{\Rlogo CHANGES IN R 3.0.1 patched}{
-+ \subsection{NEW FEATURES}{
-+ \itemize{
-+ \item The macros used for the texinfo manuals have been changed to
-+ work better with the incompatible changes made in texinfo 5.x.
-+
-+ \item The \code{example()} and \code{tools::Rd2ex()} functions now
-+ have parameters to allow them to ignore \verb{\dontrun} markup in
-+ examples. (Suggested by Peter Solymos.)
-+ }
-+ }
-+
-+ \subsection{C-LEVEL FACILITIES}{
-+ \itemize{
-+ \item \file{Rdefines.h} has been tweaked so it can be included in
-+ C++ code with \file{R_exts/Boolean.h} (which is included by
-+ \file{R.h}). Note though that \file{Rdefines.h} is not kept
-+ up-to-date, and \file{Rinternals.h} is preferred for new code.
-+ }
-+ }
-+
-+ \subsection{BUG FIXES}{
-+ \itemize{
-+ \item \code{help.request()} could not determine the current version
-+ of \R on CRAN. (\PR{15241})
-+
-+ \item On Windows, \code{file.info()} failed on root directories unless
-+ the path was terminated with an explicit \code{"."}. (\PR{15302})
-+
-+ \item The \code{regmatches<-()} replacement function mishandled
-+ results coming from \code{regexpr()}. (\PR{15311})
-+
-+ \item Documentation for \code{setClass} and
-+ \code{representation} still suggested the deprecated argument
-+ \code{representation=}. (\PR{15312})
-+
-+ \item \command{R CMD config} failed in an installed build of \R
-+ 3.0.1 (only) when a sub-architecture was used. (Reported by
-+ Berwin Turlach.)
-+
-+ \item On Windows, the installer modified the \file{etc/Rconsole} and
-+ \file{etc/Rprofile.site} files even when default options were
-+ chosen. (Reported by Tal Galili.)
-+ }
-+ }
-+}
-+
- \section{\Rlogo CHANGES IN R 3.0.1}{
- \subsection{NEW FEATURES}{
- \itemize{
-@@ -142,28 +189,28 @@
- \item \code{as.dendrogram()}'s \code{hclust} method uses less
- memory and hence gets considerably faster for large (n ~ 1000)
- clusterings, thanks to Daniel Müllner. (\PR{15174})
--
-+
- \item The return value when all workers failed from
- \code{parallel::mclapply(mc.presechedule = TRUE)} was a list of
- strings and not of error objects. (Spotted by Karl Forner and
-- Bernd Bischl.)
--
-+ Bernd Bischl.)
-+
- \item In \R 3.0.0, when \code{help()} found multiple pages with
- the same alias, the HTML display of all the selections was not
-- produced. (\PR{15282})
--
-+ produced. (\PR{15282})
-+
- \item \code{splinefun(method="monoH.FC")} now produces a
- function with first argument named \code{x} and allows
-- \code{deriv=3}, as documented. (\PR{15273})
--
-- \item \code{summaryRprof()} would only read the first
-+ \code{deriv=3}, as documented. (\PR{15273})
-+
-+ \item \code{summaryRprof()} would only read the first
- \code{chunksize} lines of an \code{Rprof} file produced with
- \code{line.profiling=TRUE}. By default, this is the first 100
- seconds. (\PR{15288})
--
-+
- \item \code{lsfit()} produced an incorrect error message when
- argument \code{x} had more columns than rows or \code{x} had a
-- different number of rows than \code{y}. (Spotted by Renaud Gaujoux.)
-+ different number of rows than \code{y}. (Spotted by Renaud Gaujoux.)
-
- \item Binary operations on equal length vectors copied the
- class name from the second operand when the first had no
-diff -ruN R-3.0.1/doc/html/NEWS.html R-patched/doc/html/NEWS.html
---- doc/html/NEWS.html 2013-05-16 03:05:47.000000000 -0400
-+++ doc/html/NEWS.html 2013-05-26 18:10:20.000000000 -0400
-@@ -8,6 +8,76 @@
-
- <h2> R News</h2>
-
-+<h3><img src="../help/figures/../../html/logo.jpg" alt="../../html/logo.jpg" /> CHANGES IN R 3.0.1 patched</h3>
-+
-+
-+
-+<h4>NEW FEATURES</h4>
-+
-+
-+<ul>
-+<li><p> The macros used for the texinfo manuals have been changed to
-+work better with the incompatible changes made in texinfo 5.x.
-+</p>
-+</li>
-+<li><p> The <code>example()</code> and <code>tools::Rd2ex()</code> functions now
-+have parameters to allow them to ignore </p>
-+<PRE>\dontrun</PRE> markup in
-+examples. (Suggested by Peter Solymos.)
-+</li></ul>
-+
-+
-+
-+
-+<h4>C-LEVEL FACILITIES</h4>
-+
-+
-+<ul>
-+<li> <p>‘<span class="file">Rdefines.h</span>’ has been tweaked so it can be included in
-+C++ code with ‘<span class="file">R_exts/Boolean.h</span>’ (which is included by
-+‘<span class="file">R.h</span>’). Note though that ‘<span class="file">Rdefines.h</span>’ is not kept
-+up-to-date, and ‘<span class="file">Rinternals.h</span>’ is preferred for new code.
-+</p>
-+</li></ul>
-+
-+
-+
-+
-+<h4>BUG FIXES</h4>
-+
-+
-+<ul>
-+<li> <p><code>help.request()</code> could not determine the current version
-+of <font face="Courier New,Courier" color="#666666"><b>R</b></font> on CRAN. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15241">PR#15241</a>)
-+</p>
-+</li>
-+<li><p> On Windows, <code>file.info()</code> failed on root directories unless
-+the path was terminated with an explicit <code>"."</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15302">PR#15302</a>)
-+</p>
-+</li>
-+<li><p> The <code>regmatches<-()</code> replacement function mishandled
-+results coming from <code>regexpr()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15311">PR#15311</a>)
-+</p>
-+</li>
-+<li><p> Documentation for <code>setClass</code> and
-+<code>representation</code> still suggested the deprecated argument
-+<code>representation=</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15312">PR#15312</a>)
-+</p>
-+</li>
-+<li> <p><CODE>R CMD config</CODE> failed in an installed build of <font face="Courier New,Courier" color="#666666"><b>R</b></font>
-+3.0.1 (only) when a sub-architecture was used. (Reported by
-+Berwin Turlach.)
-+</p>
-+</li>
-+<li><p> On Windows, the installer modified the ‘<span class="file">etc/Rconsole</span>’ and
-+‘<span class="file">etc/Rprofile.site</span>’ files even when default options were
-+chosen. (Reported by Tal Galili.)
-+</p>
-+</li></ul>
-+
-+
-+
-+
- <h3><img src="../help/figures/../../html/logo.jpg" alt="../../html/logo.jpg" /> CHANGES IN R 3.0.1</h3>
-
-
-@@ -191,20 +261,20 @@
- <li><p> The return value when all workers failed from
- <code>parallel::mclapply(mc.presechedule = TRUE)</code> was a list of
- strings and not of error objects. (Spotted by Karl Forner and
--Bernd Bischl.)
-+Bernd Bischl.)
- </p>
- </li>
- <li><p> In <font face="Courier New,Courier" color="#666666"><b>R</b></font> 3.0.0, when <code>help()</code> found multiple pages with
- the same alias, the HTML display of all the selections was not
--produced. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15282">PR#15282</a>)
-+produced. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15282">PR#15282</a>)
- </p>
- </li>
- <li> <p><code>splinefun(method="monoH.FC")</code> now produces a
- function with first argument named <code>x</code> and allows
--<code>deriv=3</code>, as documented. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15273">PR#15273</a>)
-+<code>deriv=3</code>, as documented. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15273">PR#15273</a>)
- </p>
- </li>
--<li> <p><code>summaryRprof()</code> would only read the first
-+<li> <p><code>summaryRprof()</code> would only read the first
- <code>chunksize</code> lines of an <code>Rprof</code> file produced with
- <code>line.profiling=TRUE</code>. By default, this is the first 100
- seconds. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15288">PR#15288</a>)
-@@ -212,7 +282,7 @@
- </li>
- <li> <p><code>lsfit()</code> produced an incorrect error message when
- argument <code>x</code> had more columns than rows or <code>x</code> had a
--different number of rows than <code>y</code>. (Spotted by Renaud Gaujoux.)
-+different number of rows than <code>y</code>. (Spotted by Renaud Gaujoux.)
- </p>
- </li>
- <li><p> Binary operations on equal length vectors copied the
-diff -ruN R-3.0.1/doc/html/R-admin.html R-patched/doc/html/R-admin.html
---- doc/html/R-admin.html 2013-05-16 03:11:03.000000000 -0400
-+++ doc/html/R-admin.html 2013-05-26 18:15:13.000000000 -0400
-@@ -245,7 +245,7 @@
-
- <p>This is a guide to installation and administration for R.
-
-- <p>The current version of this document is 3.0.1 (2013-05-16).
-+ <p>The current version of this document is 3.0.1 Patched (2013-05-26).
-
- <p>
-
-@@ -986,7 +986,7 @@
- perhaps for some network-mounted systems).
-
- <p>Installation is <em>via</em> the installer
--<samp><span class="file">R-3.0.1-win.exe</span></samp>. Just double-click on the icon and
-+<samp><span class="file">R-3.0.1patched-win.exe</span></samp>. Just double-click on the icon and
- follow the instructions. When installing on a 64-bit version of Windows
- the options will include 32- or 64-bit versions of R (and the default is
- to install both). You can uninstall R from the Control Panel.
-@@ -1286,7 +1286,7 @@
- installation (in double quotes if it contains spaces or backslashes).
-
- <p>Both methods create an executable with a standard name such as
--<samp><span class="file">R-3.0.1-win.exe</span></samp>, so please rename it to indicate that
-+<samp><span class="file">R-3.0.1patched-win.exe</span></samp>, so please rename it to indicate that
- it is customized. If you intend to <em>distribute</em> a customized
- installer please do check that license requirements are met – note that
- the installer will state that the contents are distributed under GPL-2
-@@ -1338,21 +1338,21 @@
- make msi
- </pre>
- <p class="noindent">which will result in a file with a name like
--<samp><span class="file">R-3.0.1-win32.msi</span></samp>. This can be double-clicked to be
-+<samp><span class="file">R-3.0.1patched-win32.msi</span></samp>. This can be double-clicked to be
- installed, but those who need it will know what to do with it (usually
- by running <samp><span class="command">msiexec /i</span></samp> with additional options). Properties
- that users might want to set from the <samp><span class="command">msiexec</span></samp> command line
- include ‘<samp><span class="samp">ALLUSERS</span></samp>’, ‘<samp><span class="samp">INSTALLDIR</span></samp>’ (something like
--<samp><span class="file">c:\Program Files\R\R-3.0.1</span></samp>) and ‘<samp><span class="samp">RMENU</span></samp>’ (the path
-+<samp><span class="file">c:\Program Files\R\R-3.0.1patched</span></samp>) and ‘<samp><span class="samp">RMENU</span></samp>’ (the path
- to the ‘<samp><span class="samp">R</span></samp>’ folder on the start menu) and ‘<samp><span class="samp">STARTDIR</span></samp>’ (the
- starting directory for R shortcuts, defaulting to something like
- <samp><span class="file">c:\Users\name\Documents\R</span></samp>).
-
- <p>The MSI installer can be built both from a 32-bit build of R
--(<samp><span class="file">R-3.0.1-win32.msi</span></samp>) and from a 64-bit build of R
--(<samp><span class="file">R-3.0.1-win64.msi</span></samp>, optionally including 32-bit files
-+(<samp><span class="file">R-3.0.1patched-win32.msi</span></samp>) and from a 64-bit build of R
-+(<samp><span class="file">R-3.0.1patched-win64.msi</span></samp>, optionally including 32-bit files
- by setting the macro <code>HOME32</code>, when the name is
--<samp><span class="file">R-3.0.1-win.msi</span></samp>). Unlike the main installer, a 64-bit
-+<samp><span class="file">R-3.0.1patched-win.msi</span></samp>). Unlike the main installer, a 64-bit
- MSI installer can only be run on 64-bit Windows.
-
- <p>Thanks to David del Campo (Dept of Statistics, University of Oxford)
-@@ -1421,10 +1421,6 @@
- should run on all Macs from mid-2008 on. For older Intel Macs and some
- older versions of the OS you can install R from the sources.
-
-- <p>Note that unlike <acronym>CRAN</acronym> binary distributions of R 2.x.y,
--there is only a 64-bit version (and hence no separate <code>R64.app</code>
--application, nor <samp><span class="command">R64</span></samp>/<samp><span class="command">R32</span></samp> front-ends).
--
- <p>To install, just double-click on the icon of the file you downloaded.
- At the `Installation Type' stage, note the option to `Customize'. This
- currently shows three components (`Package Name'). Everyone will need
-@@ -1789,8 +1785,7 @@
- <acronym>CRAN</acronym> or local files.
-
- <p>Note that many binary packages including compiled code are tied to a
--particular series (e.g. R 2.15.x or 3.0.x) of R: in any case R 3.0.x
--cannot use any binary packages built for R 2.15.x or earlier.
-+particular series (e.g. R 3.0.x or 3.1.x) of R.
-
- <p>Installing source packages which do not contain compiled code should
- work with no additional tools. For others you will need the `Command
-@@ -2611,7 +2606,7 @@
- <samp><span class="file">texinfo.tex</span></samp> need to be compatible: we have seen problems with
- older TeX distributions (TeXLive 2007 and MiKTeX 2.8) used with
- <strong>texinfo</strong> 4.13. It should be possible to use <samp><span class="command">makeinfo</span></samp>
--version 5.0, but e.g.. 4.13 produces better-formatted output.
-+version 5.x.
-
- <p><a name="index-Vignettes-69"></a>The PDF documentation (including <samp><span class="file">doc/NEWS.pdf</span></samp>) and building
- vignettes needs <samp><span class="command">pdftex</span></samp> and <samp><span class="command">pdflatex</span></samp>. We require
-@@ -4693,7 +4688,7 @@
-
- <h3 class="section">D.2 The Inno Setup installer</h3>
-
--<p>To make the installer package (<samp><span class="file">R-3.0.1-win.exe</span></samp>) we
-+<p>To make the installer package (<samp><span class="file">R-3.0.1patched-win.exe</span></samp>) we
- currently require the Unicode version of Inno Setup 5.3.7 or later from
- <a href="http://jrsoftware.org/">http://jrsoftware.org/</a>. This is <em>not</em> included in
- <samp><span class="file">Rtools*.exe</span></samp>.
-diff -ruN R-3.0.1/doc/manual/R-admin.texi R-patched/doc/manual/R-admin.texi
---- doc/manual/R-admin.texi 2013-04-29 07:05:23.000000000 -0400
-+++ doc/manual/R-admin.texi 2013-05-24 18:05:06.000000000 -0400
-@@ -1473,10 +1473,6 @@
- should run on all Macs from mid-2008 on. For older Intel Macs and some
- older versions of the OS you can install @R{} from the sources.
-
--Note that unlike @acronym{CRAN} binary distributions of @R{} 2.x.y,
--there is only a 64-bit version (and hence no separate @code{R64.app}
--application, nor @command{R64}/@command{R32} front-ends).
--
- To install, just double-click on the icon of the file you downloaded.
- At the `Installation Type' stage, note the option to `Customize'. This
- currently shows three components (`Package Name'). Everyone will need
-@@ -1904,8 +1900,7 @@
- @acronym{CRAN} or local files.
-
- Note that many binary packages including compiled code are tied to a
--particular series (e.g.@: @R{} 2.15.x or 3.0.x) of @R{}: in any case @R{} 3.0.x
--cannot use any binary packages built for @R{} 2.15.x or earlier.
-+particular series (e.g.@: @R{} 3.0.x or 3.1.x) of @R{}.
-
- Installing source packages which do not contain compiled code should
- work with no additional tools. For others you will need the `Command
-@@ -2863,7 +2858,7 @@
- @file{texinfo.tex} need to be compatible: we have seen problems with
- older @TeX{} distributions (TeXLive 2007 and MiKTeX 2.8) used with
- @pkg{texinfo} 4.13. It should be possible to use @command{makeinfo}
--version 5.0, but e.g..@: 4.13 produces better-formatted output.
-+version 5.x.
-
- @cindex Vignettes
- The PDF documentation (including @file{doc/NEWS.pdf}) and building
-diff -ruN R-3.0.1/doc/manual/R-defs.texi R-patched/doc/manual/R-defs.texi
---- doc/manual/R-defs.texi 2013-04-03 18:05:07.000000000 -0400
-+++ doc/manual/R-defs.texi 2013-05-24 18:05:06.000000000 -0400
-@@ -17,16 +17,18 @@
- @acronym{HTML}
- @end macro
-
-- at macro eqn {t, a}
- @iftex
-+ at macro eqn {t, a}
- @tex
- $\t\$%
- @end tex
-+ at end macro
- @end iftex
- @ifnottex
--\a\@c
-- at end ifnottex
-+ at macro eqn {t, a}
-+\a\
- @end macro
-+ at end ifnottex
-
- @macro pkg {p}
- @strong{\p\}
-diff -ruN R-3.0.1/doc/manual/R-exts.R R-patched/doc/manual/R-exts.R
---- doc/manual/R-exts.R 2011-06-17 06:39:34.000000000 -0400
-+++ doc/manual/R-exts.R 2013-05-26 18:05:04.000000000 -0400
-@@ -33,9 +33,6 @@
- u <- rep(1, 5)
- conv(u, u)
-
--conv <- function(a, b) .Call("convolve2b", a, b)
--conv(u, u)
--
- convE <- function(a, b) .External("convolveE", a, b)
- convE(u, u)
-
-@@ -71,7 +68,7 @@
-
- ## ----- numerical derivatives -----
-
--numeric.deriv <- function(expr, theta, rho=sys.frame(sys.parent()))
-+numeric.deriv <- function(expr, theta, rho = sys.frame(sys.parent()))
- {
- eps <- sqrt(.Machine$double.eps)
- ans <- eval(substitute(expr), rho)
-diff -ruN R-3.0.1/doc/manual/R-exts.c R-patched/doc/manual/R-exts.c
---- doc/manual/R-exts.c 2013-02-04 18:05:11.000000000 -0500
-+++ doc/manual/R-exts.c 2013-05-26 18:05:04.000000000 -0400
-@@ -13,27 +13,22 @@
- /* second version */
- SEXP out(SEXP x, SEXP y)
- {
-- int i, j, nx = length(x), ny = length(y);
-- double tmp, *rx = REAL(x), *ry = REAL(y), *rans;
-- SEXP ans, dim, dimnames;
--
-- PROTECT(ans = allocMatrix(REALSXP, nx, ny));
-- rans = REAL(ans);
-- for(i = 0; i < nx; i++) {
-- tmp = rx[i];
-- for(j = 0; j < ny; j++)
-+ int nx = length(x), ny = length(y);
-+ SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny));
-+ double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans);
-+
-+ for(int i = 0; i < nx; i++) {
-+ double tmp = rx[i];
-+ for(int j = 0; j < ny; j++)
- rans[i + nx*j] = tmp * ry[j];
- }
-- PROTECT(dim = allocVector(INTSXP, 2));
-- INTEGER(dim)[0] = nx; INTEGER(dim)[1] = ny;
-- setAttrib(ans, R_DimSymbol, dim);
-
-- PROTECT(dimnames = allocVector(VECSXP, 2));
-+ SEXP dimnames = PROTECT(allocVector(VECSXP, 2));
- SET_VECTOR_ELT(dimnames, 0, getAttrib(x, R_NamesSymbol));
- SET_VECTOR_ELT(dimnames, 1, getAttrib(y, R_NamesSymbol));
- setAttrib(ans, R_DimNamesSymbol, dimnames);
-- UNPROTECT(3);
-- return(ans);
-+ UNPROTECT(2);
-+ return ans;
- }
-
- /* get the list element named str, or return NULL */
-@@ -60,69 +55,48 @@
- error("rho should be an environment");
- ans = findVar(install(CHAR(STRING_ELT(name, 0))), rho);
- Rprintf("first value is %f\n", REAL(ans)[0]);
-- return(R_NilValue);
-+ return R_NilValue;
- }
-
- /* ----- Convolution via .Call ----- */
-
--#include <Rdefines.h>
-+#include <Rinternals.h>
- SEXP convolve2(SEXP a, SEXP b)
- {
-- int i, j, na, nb, nab;
-+ int na, nb, nab;
- double *xa, *xb, *xab;
- SEXP ab;
-
-- PROTECT(a = AS_NUMERIC(a));
-- PROTECT(b = AS_NUMERIC(b));
-- na = LENGTH(a); nb = LENGTH(b); nab = na + nb - 1;
-- PROTECT(ab = NEW_NUMERIC(nab));
-- xa = NUMERIC_POINTER(a); xb = NUMERIC_POINTER(b);
-- xab = NUMERIC_POINTER(ab);
-- for(i = 0; i < nab; i++) xab[i] = 0.0;
-- for(i = 0; i < na; i++)
-- for(j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j];
-- UNPROTECT(3);
-- return(ab);
--}
--
--SEXP convolve2b(SEXP a, SEXP b)
--{
-- int i, j, na, nb, nab;
-- double *xa, *xb, *xab;
-- SEXP ab;
--
-- PROTECT(a = coerceVector(a, REALSXP));
-- PROTECT(b = coerceVector(b, REALSXP));
-+ a = PROTECT(coerceVector(a, REALSXP));
-+ b = PROTECT(coerceVector(b, REALSXP));
- na = length(a); nb = length(b); nab = na + nb - 1;
-- PROTECT(ab = allocVector(REALSXP, nab));
-- xa = REAL(a); xb = REAL(b);
-- xab = REAL(ab);
-- for(i = 0; i < nab; i++) xab[i] = 0.0;
-- for(i = 0; i < na; i++)
-- for(j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j];
-+ ab = PROTECT(allocVector(REALSXP, nab));
-+ xa = REAL(a); xb = REAL(b); xab = REAL(ab);
-+ for(int i = 0; i < nab; i++) xab[i] = 0.0;
-+ for(int i = 0; i < na; i++)
-+ for(int j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j];
- UNPROTECT(3);
-- return(ab);
-+ return ab;
- }
-
- /* ----- Convolution via .External ----- */
-
- SEXP convolveE(SEXP args)
- {
-- int i, j, na, nb, nab;
-+ int na, nb, nab;
- double *xa, *xb, *xab;
- SEXP a, b, ab;
-
-- PROTECT(a = coerceVector(CADR(args), REALSXP));
-- PROTECT(b = coerceVector(CADDR(args), REALSXP));
-+ a = PROTECT(coerceVector(CADR(args), REALSXP));
-+ b = PROTECT(coerceVector(CADDR(args), REALSXP));
- na = length(a); nb = length(b); nab = na + nb - 1;
-- PROTECT(ab = allocVector(REALSXP, nab));
-- xa = REAL(a); xb = REAL(b);
-- xab = REAL(ab);
-- for(i = 0; i < nab; i++) xab[i] = 0.0;
-- for(i = 0; i < na; i++)
-- for(j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j];
-+ ab = PROTECT(allocVector(REALSXP, nab));
-+ xa = REAL(a); xb = REAL(b); xab = REAL(ab);
-+ for(int i = 0; i < nab; i++) xab[i] = 0.0;
-+ for(int i = 0; i < na; i++)
-+ for(int j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j];
- UNPROTECT(3);
-- return(ab);
-+ return ab;
- }
-
- /* ----- Show arguments ----- */
-@@ -160,7 +134,7 @@
- Rprintf("[%d] '%s' R type\n", i+1, name);
- }
- }
-- return(R_NilValue);
-+ return R_NilValue;
- }
-
- SEXP showArgs1(SEXP largs)
-@@ -193,45 +167,45 @@
- Rprintf("[%d] '%s' R type\n", i+1, name);
- }
- }
-- return(R_NilValue);
-+ return R_NilValue;
- }
-
- /* ----- Skeleton lapply ----- */
-
- SEXP lapply(SEXP list, SEXP expr, SEXP rho)
- {
-- int i, n = length(list);
-+ int n = length(list);
- SEXP ans;
-
- if(!isNewList(list)) error("'list' must be a list");
- if(!isEnvironment(rho)) error("'rho' should be an environment");
-- PROTECT(ans = allocVector(VECSXP, n));
-- for(i = 0; i < n; i++) {
-+ ans = PROTECT(allocVector(VECSXP, n));
-+ for(int i = 0; i < n; i++) {
- defineVar(install("x"), VECTOR_ELT(list, i), rho);
- SET_VECTOR_ELT(ans, i, eval(expr, rho));
- }
- setAttrib(ans, R_NamesSymbol, getAttrib(list, R_NamesSymbol));
- UNPROTECT(1);
-- return(ans);
-+ return ans;
- }
-
- SEXP lapply2(SEXP list, SEXP fn, SEXP rho)
- {
-- int i, n = length(list);
-+ int n = length(list);
- SEXP R_fcall, ans;
-
- if(!isNewList(list)) error("'list' must be a list");
- if(!isFunction(fn)) error("'fn' must be a function");
- if(!isEnvironment(rho)) error("'rho' should be an environment");
-- PROTECT(R_fcall = lang2(fn, R_NilValue));
-- PROTECT(ans = allocVector(VECSXP, n));
-- for(i = 0; i < n; i++) {
-+ R_fcall = PROTECT(lang2(fn, R_NilValue));
-+ ans = PROTECT(allocVector(VECSXP, n));
-+ for(int i = 0; i < n; i++) {
- SETCADR(R_fcall, VECTOR_ELT(list, i));
- SET_VECTOR_ELT(ans, i, eval(R_fcall, rho));
- }
- setAttrib(ans, R_NamesSymbol, getAttrib(list, R_NamesSymbol));
- UNPROTECT(2);
-- return(ans);
-+ return ans;
- }
-
- /* ----- Zero-finding ----- */
-@@ -239,7 +213,7 @@
- SEXP mkans(double x)
- {
- SEXP ans;
-- PROTECT(ans = allocVector(REALSXP, 1));
-+ ans = PROTECT(allocVector(REALSXP, 1));
- REAL(ans)[0] = x;
- UNPROTECT(1);
- return ans;
-@@ -248,7 +222,7 @@
- double feval(double x, SEXP f, SEXP rho)
- {
- defineVar(install("x"), mkans(x), rho);
-- return(REAL(eval(f, rho))[0]);
-+ return REAL(eval(f, rho))[0];
- }
-
- SEXP zero(SEXP f, SEXP guesses, SEXP stol, SEXP rho)
-@@ -285,7 +259,7 @@
- {
- SEXP theta, expr, rho, ans, ans1, gradient, par, dimnames;
- double tt, xx, delta, eps = sqrt(DOUBLE_EPS), *rgr, *rans;
-- int start, i, j;
-+ int i, start;
-
- expr = CADR(args);
- if(!isString(theta = CADDR(args)))
-@@ -293,8 +267,8 @@
- if(!isEnvironment(rho = CADDDR(args)))
- error("rho should be an environment");
-
-- PROTECT(ans = coerceVector(eval(expr, rho), REALSXP));
-- PROTECT(gradient = allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta)));
-+ ans = PROTECT(coerceVector(eval(expr, rho), REALSXP));
-+ gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta)));
- rgr = REAL(gradient); rans = REAL(ans);
-
- for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(ans)) {
-@@ -303,14 +277,14 @@
- xx = fabs(tt);
- delta = (xx < 1) ? eps : xx*eps;
- REAL(par)[0] += delta;
-- PROTECT(ans1 = coerceVector(eval(expr, rho), REALSXP));
-- for(j = 0; j < LENGTH(ans); j++)
-+ ans1 = PROTECT(coerceVector(eval(expr, rho), REALSXP));
-+ for(int j = 0; j < LENGTH(ans); j++)
- rgr[j + start] = (REAL(ans1)[j] - rans[j])/delta;
- REAL(par)[0] = tt;
- UNPROTECT(2); /* par, ans1 */
- }
-
-- PROTECT(dimnames = allocVector(VECSXP, 2));
-+ dimnames = PROTECT(allocVector(VECSXP, 2));
- SET_VECTOR_ELT(dimnames, 1, theta);
- dimnamesgets(gradient, dimnames);
- setAttrib(ans, install("gradient"), gradient);
-diff -ruN R-3.0.1/doc/manual/R-exts.texi R-patched/doc/manual/R-exts.texi
---- doc/manual/R-exts.texi 2013-04-22 18:05:03.000000000 -0400
-+++ doc/manual/R-exts.texi 2013-05-26 18:05:04.000000000 -0400
-@@ -219,13 +219,19 @@
- @pxref{Lazy loading, , Lazy loading, R-ints, R Internals}.)
- @end ifset
-
-+ at cindex CRAN
-+ at acronym{CRAN} is a network of WWW sites holding the @R{} distributions
-+and contributed code, especially @R{} packages. Users of @R{} are
-+encouraged to join in the collaborative project and to submit their own
-+packages to @acronym{CRAN}: current instructions are linked from
-+ at uref{http://CRAN.R-project.org/banner.shtml#submitting}.
-+
-
- @menu
- * Package structure::
- * Configure and cleanup::
- * Checking and building packages::
- * Writing package vignettes::
--* Submitting a package to CRAN::
- * Package namespaces::
- * Writing portable packages::
- * Diagnostic messages::
-@@ -1236,7 +1242,7 @@
- @end example
-
- @noindent
--then downoad the sources from
-+then download the sources from
- @uref{http://sourceforge.net/projects/tcllib/files/BWidget/} and
- at the command line run
-
-@@ -2596,7 +2602,7 @@
- who do not have access to Windows but wish to provide binaries for the
- Windows platform.
-
-- at node Writing package vignettes, Submitting a package to CRAN, Checking and building packages, Creating R packages
-+ at node Writing package vignettes, Package namespaces, Checking and building packages, Creating R packages
- @section Writing package vignettes
- @cindex vignettes
- @cindex Sweave
-@@ -2854,21 +2860,8 @@
- See the @code{?tools::vignetteEngine} help topic for details
- on engine registration.
-
-- at node Submitting a package to CRAN, Package namespaces, Writing package vignettes, Creating R packages
-- at section Submitting a package to @acronym{CRAN}
-- at cindex CRAN
-- at cindex CRAN submission
-- at cindex Submitting to CRAN
--
-- at acronym{CRAN} is a network of WWW sites holding the @R{} distributions
--and contributed code, especially @R{} packages. Users of @R{} are
--encouraged to join in the collaborative project and to submit their own
--packages to @acronym{CRAN}.
-
--Current submission instructions are linked from
-- at uref{http://CRAN.R-project.org/banner.shtml#submitting}.
--
-- at node Package namespaces, Writing portable packages, Submitting a package to CRAN, Creating R packages
-+ at node Package namespaces, Writing portable packages, Writing package vignettes, Creating R packages
- @section Package namespaces
- @cindex namespaces
-
-@@ -7287,12 +7280,12 @@
- @group
- void convolve(double *a, int *na, double *b, int *nb, double *ab)
- @{
-- int i, j, nab = *na + *nb - 1;
-+ int nab = *na + *nb - 1;
-
-- for(i = 0; i < nab; i++)
-+ for(int i = 0; i < nab; i++)
- ab[i] = 0.0;
-- for(i = 0; i < *na; i++)
-- for(j = 0; j < *nb; j++)
-+ for(int i = 0; i < *na; i++)
-+ for(int j = 0; j < *nb; j++)
- ab[i + j] += a[i] * b[j];
- @}
- @end group
-@@ -8066,28 +8059,24 @@
- package @pkg{packB} is incorporated when package @pkg{packA} is
- installed, we only need to find the static library at install time for
- package @pkg{packB}. The only issue is to find package @pkg{packB}, and
--for that we can ask @R{} by something like (lines broken for display here)
-+for that we can ask @R{} by something like (long lines broken for display here)
-
- @example
--PKGB_PATH=`echo 'cat(system.file("libs", .Platform$$r_arch,
-- package="packB", mustWork=TRUE))' \
-+PKGB_PATH=`echo 'library(packB);
-+ cat(system.file("libs", package="packB", mustWork=TRUE))' \
- | "$@{R_HOME@}/bin/R" --vanilla --slave`
--PKG_LIBS="$(PKGB_PATH)/libpackB.a"
-+PKG_LIBS="$(PKGB_PATH)$(R_ARCH)/libpackB.a"
- @end example
-
-- at noindent
--which will give an empty path component if sub-architectures are not in
--use (but that works on current platforms).
--
- For a dynamic library @file{packB/libs/libpackB.so}
- (@file{packB/libs/libpackB.dylib} on OS X: note that you cannot link to
- a shared object, @file{.so} on that platform) we could use
-
- @example
--PKGB_PATH=`echo 'cat(system.file("libs", .Platform$$r_arch,
-- package="packB", mustWork=TRUE))' \
-+PKGB_PATH=`echo 'library(packB);
-+ cat(system.file("libs", package="packB", mustWork=TRUE))' \
- | "$@{R_HOME@}/bin/R" --vanilla --slave`
--PKG_LIBS=-L"$(PKGB_PATH)" -lpackB
-+PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -lpackB
- @end example
-
- @noindent
-@@ -8105,9 +8094,10 @@
- this can be done by e.g.@:
-
- @example
--PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="packB"))' \
-+PKGB_PATH=`echo 'library(packB);
-+ cat(system.file("libs", package="packB", mustWork=TRUE)))' \
- | "$@{R_HOME@}/bin/R" --vanilla --slave`
--PKG_LIBS=-L"$(PKGB_PATH)" -rpath "$(PKGB_PATH)" -lpackB
-+PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -rpath "$(PKGB_PATH)$(R_ARCH)" -lpackB
- @end example
-
- @noindent
-@@ -8154,9 +8144,10 @@
- where it is by something like
-
- @example
--PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="packB"))' \
-+PKGB_PATH=`echo 'library(packB);
-+ cat(system.file("libs", package="packB", mustWork=TRUE))' \
- | rterm --vanilla --slave`
--PKG_LIBS= -L"$(PKGB_PATH)"$(R_ARCH) -lexB
-+PKG_LIBS= -L"$(PKGB_PATH)$(R_ARCH)" -lexB
- @end example
-
- Another possibility is to use an import library, shipping with package
-@@ -8182,7 +8173,7 @@
- @file{packB.dll} or @file{packB.dll} depends on it) and @pkg{packB} has
- been loaded before @pkg{packA}, then nothing more needs to be done as
- @file{exB.dll} will already be loaded into the @R{} executable. (This
--is the most common scenario).
-+is the most common scenario.)
-
- More generally, we can use the @code{DLLpath} argument to
- @code{library.dynam} to ensure that @code{exB.dll} is found, for example
-@@ -8209,9 +8200,8 @@
- @code{.Call} and @code{.External} functions. The syntax for the calling
- function in @R{} in each case is similar to that of @code{.C}, but the
- two functions have different C interfaces. Generally the @code{.Call}
--interface (which is modelled on the interface of the same name in @Sl{}
--version 4) is a little simpler to use, but @code{.External} is a little
--more general.
-+interface is simpler to use, but @code{.External} is a little more
-+general.
- @findex .Call
- @findex .External
-
-@@ -8259,48 +8249,39 @@
- Here @code{args} is a @code{LISTSXP}, a Lisp-style pairlist from which
- the arguments can be extracted.
-
--In each case the @R{} objects are available for manipulation @emph{via} a set
--of functions and macros defined in the header file @file{Rinternals.h}
--or some S4-compatibility macros defined in @file{Rdefines.h}. See
-- at ref{Interface functions .Call and .External} for details on
-- at code{.Call} and @code{.External}.
-+In each case the @R{} objects are available for manipulation @emph{via}
-+a set of functions and macros defined in the header file
-+ at file{Rinternals.h} or some @Sl{}-compatibility macros at footnote{That is,
-+similar to those defined in @Sl{} version 4 from the 1990s: these are
-+not kept up to date and are not recommended for new projects.} defined
-+in @file{Rdefines.h}. See @ref{Interface functions .Call and .External}
-+for details on @code{.Call} and @code{.External}.
-
- Before you decide to use @code{.Call} or @code{.External}, you should
- look at other alternatives. First, consider working in interpreted @R{}
- code; if this is fast enough, this is normally the best option. You
- should also see if using @code{.C} is enough. If the task to be
- performed in C is simple enough involving only atomic vectors and
--requiring no call to @R{}, @code{.C} suffices. The new interfaces are
--relatively recent additions to @Sl{} and @R{}, and a great deal of
--useful code has been written using just @code{.C} before they were
--available. The @code{.Call} and @code{.External} interfaces allow much
--more control, but they also impose much greater responsibilities so need
--to be used with care. Neither @code{.Call} nor @code{.External} copy
--their arguments: you should treat arguments you receive through these
-+requiring no call to @R{}, @code{.C} suffices. A great deal of useful
-+code was written using just @code{.C} before @code{.Call} and
-+ at code{.External} were available. These interfaces allow much more
-+control, but they also impose much greater responsibilities so need to
-+be used with care. Neither @code{.Call} nor @code{.External} copy their
-+arguments: you should treat arguments you receive through these
- interfaces as read-only.
-
--There are two approaches that can be taken to handling @R{} objects from
--within C code. The first (historically) is to use the macros and
--functions that have been used to implement the core parts of @R{}
--through @code{.Internal} calls. A public at footnote{ @pxref{The R API}:
--note that these are not all part of the API.} subset of these is
--defined in the header file @file{Rinternals.h} in the directory
-- at file{@var{R_INCLUDE_DIR}} (default @file{@var{R_HOME}/include}) that
--should be available on any @R{} installation.
--
--Another approach is to use @R{} versions of the macros and functions
--defined for the @Sl{} version 4 interface @code{.Call}, which are
--defined in the header file @file{Rdefines.h}. This is a somewhat
--simpler approach, and is to be preferred if the code is intended to be
--shared with @Sl{}. However, it is less well documented and even less
--tested. Note too that some idiomatic S4 constructions with these macros
--(such as assigning elements of character vectors or lists) are invalid
--in @R{}.
--
--A substantial amount of @R{} is implemented using the functions and
--macros described here, so the @R{} source code provides a rich source of
--examples and ``how to do it'': do make use of the source code for
--inspirational examples.
-+To handle @R{} objects from within C code we use the macros and functions
-+that have been used to implement the core parts of @R{}. A
-+public at footnote{ @pxref{The R API}: note that these are not all part of
-+the API.} subset of these is defined in the header file
-+ at file{Rinternals.h} in the directory @file{@var{R_INCLUDE_DIR}} (default
-+ at file{@var{R_HOME}/include}) that should be available on any @R{}
-+installation.
-+
-+A substantial amount of @R{}, including the standard packages, is
-+implemented using the functions and macros described here, so the @R{}
-+source code provides a rich source of examples and ``how to do it'': do
-+make use of the source code for inspirational examples.
-
- It is necessary to know something about how @R{} objects are handled in
- C code. All the @R{} objects you will deal with will be handled with
-@@ -8374,8 +8355,7 @@
- warn about @code{"stack imbalance in .Call"} (or @code{.External}) if
- the housekeeping is wrong.
-
--Here is a small example of creating an @R{} numeric vector in C code.
--First we use the macros in @file{Rinternals.h}:
-+Here is a small example of creating an @R{} numeric vector in C code:
-
- @example
- @group
-@@ -8384,30 +8364,13 @@
-
- SEXP ab;
- ....
-- PROTECT(ab = allocVector(REALSXP, 2));
-+ ab = PROTECT(allocVector(REALSXP, 2));
- REAL(ab)[0] = 123.45;
- REAL(ab)[1] = 67.89;
- UNPROTECT(1);
- @end group
- @end example
-
-- at noindent
--and then those in @file{Rdefines.h}:
--
-- at example
-- at group
--#include <R.h>
--#include <Rdefines.h>
--
-- SEXP ab;
-- ....
-- PROTECT(ab = NEW_NUMERIC(2));
-- NUMERIC_POINTER(ab)[0] = 123.45;
-- NUMERIC_POINTER(ab)[1] = 67.89;
-- UNPROTECT(1);
-- at end group
-- at end example
--
- Now, the reader may ask how the @R{} object could possibly get removed
- during those manipulations, as it is just our C code that is running.
- As it happens, we can do without the protection in this example, but in
-@@ -8448,8 +8411,8 @@
- PROTECT_INDEX ipx;
-
- ....
-- PROTECT_WITH_INDEX(s = eval(OS->R_fcall, OS->R_env), &ipx);
-- REPROTECT(s = coerceVector(s, REALSXP), ipx);
-+ s = PROTECT_WITH_INDEX(eval(OS->R_fcall, OS->R_env), &ipx);
-+ s = REPROTECT(coerceVector(s, REALSXP), ipx);
- @end example
-
- Note that it is dangerous to mix @code{UNPROTECT_PTR} with
-@@ -8463,10 +8426,7 @@
-
- For many purposes it is sufficient to allocate @R{} objects and
- manipulate those. There are quite a few @code{alloc at var{Xxx}} functions
--defined in @file{Rinternals.h}---you may want to explore them. These
--allocate @R{} objects of various types, and for the standard vector
--types there are equivalent @code{NEW_ at var{XXX}} macros defined in
-- at file{Rdefines.h}.
-+defined in @file{Rinternals.h}---you may want to explore them.
-
- If storage is required for C objects during the calculations this is
- best allocating by calling @code{R_alloc}; @pxref{Memory allocation}.
-@@ -8479,12 +8439,10 @@
- @cindex Details of R types
-
- Users of the @file{Rinternals.h} macros will need to know how the @R{}
--types are known internally: if the @file{Rdefines.h} macros are used
--then S4-compatible names are used.
--
--The different @R{} data types are represented in C by @dfn{SEXPTYPE}.
--Some of these are familiar from @R{} and some are internal data types.
--The usual @R{} object modes are given in the table.
-+types are known internally. The different @R{} data types are
-+represented in C by @dfn{SEXPTYPE}. Some of these are familiar from
-+ at R{} and some are internal data types. The usual @R{} object modes are
-+given in the table.
-
- @quotation
- @multitable {SEXPTYPE} {numeric with storage mode integer integer}
-@@ -8519,25 +8477,17 @@
- and @code{isString} to do type checking. See the header file
- @file{Rinternals.h} for definitions of other such functions. All of
- these take a @code{SEXP} as argument and return 1 or 0 to indicate
-- at var{TRUE} or @var{FALSE}. Once again there are two ways to do this,
--and @file{Rdefines.h} has macros such as @code{IS_NUMERIC}.
-+ at var{TRUE} or @var{FALSE}.
-
- What happens if the @code{SEXP} is not of the correct type? Sometimes
- you have no other option except to generate an error. You can use the
- function @code{error} for this. It is usually better to coerce the
- object to the correct type. For example, if you find that an
- @code{SEXP} is of the type @code{INTEGER}, but you need a @code{REAL}
--object, you can change the type by using, equivalently,
--
-- at example
--PROTECT(@var{newSexp} = coerceVector(@var{oldSexp}, REALSXP));
-- at end example
--
-- at noindent
--or
-+object, you can change the type by using
-
- @example
--PROTECT(@var{newSexp} = AS_NUMERIC(@var{oldSexp}));
-+ at var{newSexp} = PROTECT(coerceVector(@var{oldSexp}, REALSXP));
- @end example
-
- @noindent
-@@ -8594,19 +8544,16 @@
-
- SEXP out(SEXP x, SEXP y)
- @{
-- int i, j, nx = length(x), ny = length(y);
-- double tmp, *rx = REAL(x), *ry = REAL(y), *rans;
-- SEXP ans;
--
-- PROTECT(ans = allocMatrix(REALSXP, nx, ny));
-- rans = REAL(ans);
-- for(i = 0; i < nx; i++) @{
-- tmp = rx[i];
-- for(j = 0; j < ny; j++)
-+ int nx = length(x), ny = length(y);
-+ SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny));
-+ double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans);
-+ for(int i = 0; i < nx; i++) @{
-+ double tmp = rx[i];
-+ for(int j = 0; j < ny; j++)
- rans[i + nx*j] = tmp * ry[j];
- @}
- UNPROTECT(1);
-- return(ans);
-+ return ans;
- @}
- @end group
- @end example
-@@ -8626,29 +8573,17 @@
- @group
- SEXP out(SEXP x, SEXP y)
- @{
-- int i, j, nx = length(x), ny = length(y);
-- double tmp, *rx = REAL(x), *ry = REAL(y), *rans;
-- SEXP ans, dim, dimnames;
-- at end group
--
-- at group
-- PROTECT(ans = allocVector(REALSXP, nx*ny));
-- rans = REAL(ans);
-- for(i = 0; i < nx; i++) @{
-- tmp = rx[i];
-- for(j = 0; j < ny; j++)
-- rans[i + nx*j] = tmp * ry[j];
-+ int nx = length(x), ny = length(y);
-+ SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny));
-+ double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans);
-+
-+ for(int i = 0; i < nx; i++) @{
-+ double tmp = rx[i];
-+ for(int j = 0; j < ny; j++)
-+ rans[i + nx*j] = tmp * ry[j];
- @}
-- at end group
-
-- at group
-- PROTECT(dim = allocVector(INTSXP, 2));
-- INTEGER(dim)[0] = nx; INTEGER(dim)[1] = ny;
-- setAttrib(ans, R_DimSymbol, dim);
-- at end group
--
-- at group
-- PROTECT(dimnames = allocVector(VECSXP, 2));
-+ SEXP dimnames = PROTECT(allocVector(VECSXP, 2));
- SET_VECTOR_ELT(dimnames, 0, getAttrib(x, R_NamesSymbol));
- SET_VECTOR_ELT(dimnames, 1, getAttrib(y, R_NamesSymbol));
- setAttrib(ans, R_DimNamesSymbol, dimnames);
-@@ -8656,7 +8591,7 @@
-
- @group
- UNPROTECT(3);
-- return(ans);
-+ return ans;
- @}
- @end group
- @end example
-@@ -8685,7 +8620,7 @@
- @example
- @group
- SEXP version;
-- PROTECT(version = allocVector(REALSXP, 1));
-+ version = PROTECT(allocVector(REALSXP, 1));
- REAL(version)[0] = 3.0;
- setAttrib(ans, install("version"), version);
- UNPROTECT(1);
-@@ -8704,7 +8639,18 @@
- @end example
-
- @noindent
--if it is to be done frequently.
-+if it is to be done frequently.
-+
-+This example can be simplified by another convenience function:
-+
-+ at example
-+ at group
-+ SEXP version = PROTECT(ScalarReal(3.0));
-+ setAttrib(ans, install("version"), version);
-+ UNPROTECT(1);
-+ at end group
-+ at end example
-+
-
- @node Classes, Handling lists, Attributes, Handling R objects in C
- @subsection Classes
-@@ -8718,15 +8664,15 @@
- @example
- @group
- #include <R.h>
--#include <Rdefines.h>
-+#include <Rinternals.h>
- ....
- SEXP ans, dim, dimnames, class;
- ....
-- PROTECT(class = allocVector(STRSXP, 1));
-+ class = PROTECT(allocVector(STRSXP, 1));
- SET_STRING_ELT(class, 0, mkChar("mat"));
- classgets(ans, class);
- UNPROTECT(4);
-- return(ans);
-+ return ans;
- @}
- @end group
- @end example
-@@ -8852,7 +8798,7 @@
- error("rho should be an environment");
- ans = findVar(install(CHAR(STRING_ELT(name, 0))), rho);
- Rprintf("first value is %f\n", REAL(ans)[0]);
-- return(R_NilValue);
-+ return R_NilValue;
- @}
- @end group
- @end example
-@@ -9073,44 +9019,16 @@
-
- @findex .Call
-
--Let us convert our finite convolution example to use @code{.Call}, first
--using the @file{Rdefines.h} macros. The calling function in @R{} is
-+Let us convert our finite convolution example to use @code{.Call}. The
-+calling function in @R{} is
-
- @example
- conv <- function(a, b) .Call("convolve2", a, b)
- @end example
-
- @noindent
--which could hardly be simpler, but as we shall see all the type checking
--must be transferred to the C code, which is
--
-- at example
-- at group
--#include <R.h>
--#include <Rdefines.h>
--
--SEXP convolve2(SEXP a, SEXP b)
--@{
-- int i, j, na, nb, nab;
-- double *xa, *xb, *xab;
-- SEXP ab;
--
-- PROTECT(a = AS_NUMERIC(a));
-- PROTECT(b = AS_NUMERIC(b));
-- na = LENGTH(a); nb = LENGTH(b); nab = na + nb - 1;
-- PROTECT(ab = NEW_NUMERIC(nab));
-- xa = NUMERIC_POINTER(a); xb = NUMERIC_POINTER(b);
-- xab = NUMERIC_POINTER(ab);
-- for(i = 0; i < nab; i++) xab[i] = 0.0;
-- for(i = 0; i < na; i++)
-- for(j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j];
-- UNPROTECT(3);
-- return(ab);
--@}
-- at end group
-- at end example
--
--Now for the version in @file{Rinternals.h} style. Only the C code changes.
-+which could hardly be simpler, but as we shall see all the type
-+coercion is transferred to the C code, which is
-
- @example
- @group
-@@ -9119,28 +9037,24 @@
-
- SEXP convolve2(SEXP a, SEXP b)
- @{
-- int i, j, na, nb, nab;
-+ int na, nb, nab;
- double *xa, *xb, *xab;
- SEXP ab;
-
-- PROTECT(a = coerceVector(a, REALSXP));
-- PROTECT(b = coerceVector(b, REALSXP));
-+ a = PROTECT(coerceVector(a, REALSXP));
-+ b = PROTECT(coerceVector(b, REALSXP));
- na = length(a); nb = length(b); nab = na + nb - 1;
-- PROTECT(ab = allocVector(REALSXP, nab));
-- xa = REAL(a); xb = REAL(b);
-- xab = REAL(ab);
-- for(i = 0; i < nab; i++) xab[i] = 0.0;
-- for(i = 0; i < na; i++)
-- for(j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j];
-+ ab = PROTECT(allocVector(REALSXP, nab));
-+ xa = REAL(a); xb = REAL(b); xab = REAL(ab);
-+ for(int i = 0; i < nab; i++) xab[i] = 0.0;
-+ for(int i = 0; i < na; i++)
-+ for(int j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j];
- UNPROTECT(3);
-- return(ab);
-+ return ab;
- @}
- @end group
- @end example
-
-- at noindent
--This is called in exactly the same way.
--
- @node Calling .External, Missing and special values, Calling .Call, Interface functions .Call and .External
- @subsection Calling @code{.External}
-
-@@ -9169,8 +9083,8 @@
- double *xa, *xb, *xab;
- SEXP a, b, ab;
-
-- PROTECT(a = coerceVector(CADR(args), REALSXP));
-- PROTECT(b = coerceVector(CADDR(args), REALSXP));
-+ a = PROTECT(coerceVector(CADR(args), REALSXP));
-+ b = PROTECT(coerceVector(CADDR(args), REALSXP));
- ...
- @}
- @end group
-@@ -9260,7 +9174,7 @@
- Rprintf("[%d] '%s' R type\n", i+1, name);
- @}
- @}
-- return(R_NilValue);
-+ return R_NilValue;
- @}
- @end group
- @end example
-@@ -9304,8 +9218,8 @@
- @example
- @group
- ...
-- for(i = 0; i < na; i++)
-- for(j = 0; j < nb; j++)
-+ for(int i = 0; i < na; i++)
-+ for(int j = 0; j < nb; j++)
- if(ISNA(xa[i]) || ISNA(xb[j]) || ISNA(xab[i + j]))
- xab[i + j] = NA_REAL;
- else
-@@ -9360,19 +9274,19 @@
- @group
- SEXP lapply(SEXP list, SEXP expr, SEXP rho)
- @{
-- int i, n = length(list);
-+ int n = length(list);
- SEXP ans;
-
- if(!isNewList(list)) error("'list' must be a list");
- if(!isEnvironment(rho)) error("'rho' should be an environment");
-- PROTECT(ans = allocVector(VECSXP, n));
-- for(i = 0; i < n; i++) @{
-+ ans = PROTECT(allocVector(VECSXP, n));
-+ for(int i = 0; i < n; i++) @{
- defineVar(install("x"), VECTOR_ELT(list, i), rho);
- SET_VECTOR_ELT(ans, i, eval(expr, rho));
- @}
- setAttrib(ans, R_NamesSymbol, getAttrib(list, R_NamesSymbol));
- UNPROTECT(1);
-- return(ans);
-+ return ans;
- @}
- @end group
- @end example
-@@ -9387,21 +9301,21 @@
- @group
- SEXP lapply2(SEXP list, SEXP fn, SEXP rho)
- @{
-- int i, n = length(list);
-+ int n = length(list);
- SEXP R_fcall, ans;
-
- if(!isNewList(list)) error("'list' must be a list");
- if(!isFunction(fn)) error("'fn' must be a function");
- if(!isEnvironment(rho)) error("'rho' should be an environment");
-- PROTECT(R_fcall = lang2(fn, R_NilValue));
-- PROTECT(ans = allocVector(VECSXP, n));
-- for(i = 0; i < n; i++) @{
-+ R_fcall = PROTECT(lang2(fn, R_NilValue));
-+ ans = PROTECT(allocVector(VECSXP, n));
-+ for(int i = 0; i < n; i++) @{
- SETCADR(R_fcall, VECTOR_ELT(list, i));
- SET_VECTOR_ELT(ans, i, eval(R_fcall, rho));
- @}
- setAttrib(ans, R_NamesSymbol, getAttrib(list, R_NamesSymbol));
- UNPROTECT(2);
-- return(ans);
-+ return ans;
- @}
- @end group
- @end example
-@@ -9429,7 +9343,7 @@
- See do_docall for the template for this sort of thing.
- */
- SEXP s, t;
-- PROTECT(t = s = allocList(3));
-+ t = s = PROTECT(allocList(3));
- SET_TYPEOF(s, LANGSXP);
- SETCAR(t, install("print")); t = CDR(t);
- SETCAR(t, CAR(a)); t = CDR(t);
-@@ -9490,7 +9404,7 @@
- SEXP mkans(double x)
- @{
- SEXP ans;
-- PROTECT(ans = allocVector(REALSXP, 1));
-+ ans = PROTECT(allocVector(REALSXP, 1));
- REAL(ans)[0] = x;
- UNPROTECT(1);
- return ans;
-@@ -9501,7 +9415,7 @@
- double feval(double x, SEXP f, SEXP rho)
- @{
- defineVar(install("x"), mkans(x), rho);
-- return(REAL(eval(f, rho))[0]);
-+ return REAL(eval(f, rho))[0];
- @}
- @end group
-
-@@ -9605,7 +9519,7 @@
- @{
- SEXP theta, expr, rho, ans, ans1, gradient, par, dimnames;
- double tt, xx, delta, eps = sqrt(DOUBLE_EPS), *rgr, *rans;
-- int start, i, j;
-+ int i, start;
- @end group
-
- @group
-@@ -9617,20 +9531,20 @@
- @end group
-
- @group
-- PROTECT(ans = coerceVector(eval(expr, rho), REALSXP));
-- PROTECT(gradient = allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta)));
-+ ans = PROTECT(coerceVector(eval(expr, rho), REALSXP));
-+ gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta)));
- rgr = REAL(gradient); rans = REAL(ans);
- @end group
-
- @group
- for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(ans)) @{
-- PROTECT(par = findVar(install(CHAR(STRING_ELT(theta, i))), rho));
-+ par = PROTECT(findVar(install(CHAR(STRING_ELT(theta, i))), rho));
- tt = REAL(par)[0];
- xx = fabs(tt);
- delta = (xx < 1) ? eps : xx*eps;
- REAL(par)[0] += delta;
-- PROTECT(ans1 = coerceVector(eval(expr, rho), REALSXP));
-- for(j = 0; j < LENGTH(ans); j++)
-+ ans1 = PROTECT(coerceVector(eval(expr, rho), REALSXP));
-+ for(int j = 0; j < LENGTH(ans); j++)
- rgr[j + start] = (REAL(ans1)[j] - rans[j])/delta;
- REAL(par)[0] = tt;
- UNPROTECT(2); /* par, ans1 */
-@@ -9638,7 +9552,7 @@
- @end group
-
- @group
-- PROTECT(dimnames = allocVector(VECSXP, 2));
-+ dimnames = PROTECT(allocVector(VECSXP, 2));
- SET_VECTOR_ELT(dimnames, 1, theta);
- dimnamesgets(gradient, dimnames);
- setAttrib(ans, install("gradient"), gradient);
-@@ -9671,14 +9585,14 @@
- environment @code{rho}, by
-
- @example
-- PROTECT(ans = coerceVector(eval(expr, rho), REALSXP));
-+ ans = PROTECT(coerceVector(eval(expr, rho), REALSXP));
- @end example
-
- @noindent
- We then allocate space for the calculated derivative by
-
- @example
-- PROTECT(gradient = allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta)));
-+ gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta)));
- @end example
-
- @noindent
-@@ -9689,7 +9603,7 @@
- @example
- @group
- for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(ans)) @{
-- PROTECT(par = findVar(install(CHAR(STRING_ELT(theta, i))), rho));
-+ par = PROTECT(findVar(install(CHAR(STRING_ELT(theta, i))), rho));
- @end group
- @end example
-
-@@ -9710,7 +9624,7 @@
- xx = fabs(tt);
- delta = (xx < 1) ? eps : xx*eps;
- REAL(par)[0] += delta;
-- PROTECT(ans1 = coerceVector(eval(expr, rho), REALSXP));
-+ ans1 = PROTECT(coerceVector(eval(expr, rho), REALSXP));
- @end group
- @end example
-
-@@ -9725,7 +9639,7 @@
-
- @example
- @group
-- for(j = 0; j < LENGTH(ans); j++)
-+ for(int j = 0; j < LENGTH(ans); j++)
- rgr[j + start] = (REAL(ans1)[j] - rans[j])/delta;
- REAL(par)[0] = tt;
- UNPROTECT(2);
-@@ -9739,7 +9653,7 @@
-
- @example
- @group
-- PROTECT(dimnames = allocVector(VECSXP, 2));
-+ dimnames = PROTECT(allocVector(VECSXP, 2));
- SET_VECTOR_ELT(dimnames, 1, theta);
- dimnamesgets(gradient, dimnames);
- setAttrib(ans, install("gradient"), gradient);
-@@ -9785,7 +9699,7 @@
- ParseStatus status;
- ...
- if(done == 1) @{
-- PROTECT(cmdSexp = allocVector(STRSXP, 1));
-+ cmdSexp = PROTECT(allocVector(STRSXP, 1));
- SET_STRING_ELT(cmdSexp, 0, mkChar(cmd));
- cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilValue));
- if (status != PARSE_OK) @{
-@@ -9989,7 +9903,7 @@
-
- @example
- SEXP ans, ptr;
-- PROTECT(ans = allocVector(INTSXP, 1));
-+ ans = PROTECT(allocVector(INTSXP, 1));
- ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"), R_NilValue);
- PROTECT(ptr);
- R_RegisterCFinalizerEx(ptr, chanFinalizer, TRUE);
-@@ -10615,6 +10529,12 @@
- The standard packages, for example @pkg{stats}, are a rich source of
- further examples.
-
-+Passing character strings from C to FORTRAN 77 or @emph{vice versa} is
-+not portable (and to Fortran 90 or later is even less so). We have
-+found that it helps to ensure that a C string to be passed is followed
-+by several @code{nul}s (and not just the one needed as a C terminator).
-+But for maximal portability character strings in FORTRAN should be
-+avoided.
-
-
- @node Numerical analysis subroutines, Optimization, Calling C from FORTRAN and vice versa, The R API
-diff -ruN R-3.0.1/doc/manual/R-intro.texi R-patched/doc/manual/R-intro.texi
---- doc/manual/R-intro.texi 2013-04-03 18:05:07.000000000 -0400
-+++ doc/manual/R-intro.texi 2013-05-24 18:05:06.000000000 -0400
-@@ -84,7 +84,9 @@
- @top An Introduction to R
-
- This is an introduction to R (``GNU S''), a language and environment for
--statistical computing and graphics. R is similar to the award-winning S
-+statistical computing and graphics. R is similar to the
-+award-winning at footnote{ACM Software Systems award, 1998:
-+ at uref{http://awards.acm.org/award_winners/chambers_6640862.cfm}.} S
- system, which was developed at Bell Laboratories by John Chambers et al.
- It provides a wide variety of statistical and graphical techniques
- (linear and nonlinear modelling, statistical tests, time series
-@@ -149,8 +151,8 @@
- and more importantly some instant feedback on what actually happens.
-
- Many users will come to @R{} mainly for its graphical facilities.
-- at ref{Graphics} on the graphics facilities can be read at almost any time
--and need not wait until all the preceding sections have been digested.
-+ at xref{Graphics}, which can be read at almost any time and need not wait
-+until all the preceding sections have been digested.
-
- @menu
- * Introduction and preliminaries::
-@@ -1981,12 +1983,27 @@
- @node Matrix facilities, Forming partitioned matrices, Generalized transpose of an array, Arrays and matrices
- @section Matrix facilities
-
-+ at iftex
- @macro xTx{}
-- @eqn{@strong{x}^T @strong{x}, x'x}
-+ at tex
-+$@strong{x}^T @strong{x}$%
-+ at end tex
- @end macro
- @macro xxT{}
-- @eqn{@strong{x}@strong{x}^T, x x'}
-+ at tex
-+$@strong{x}@strong{x}^T$%
-+ at end tex
- @end macro
-+ at end iftex
-+
-+ at ifnottex
-+ at macro xTx{}
-+x'x
-+ at end macro
-+ at macro xxT{}
-+x x'
-+ at end macro
-+ at end ifnottex
-
- As noted above, a matrix is just an array with two subscripts. However
- it is such an important special case it needs a separate discussion.
-@@ -2047,8 +2064,7 @@
- result. The matrix @xxT{} may be calculated either by @code{cbind(x)
- %*% x} or @code{x %*% rbind(x)} since the result of @code{rbind()} or
- @code{cbind()} is always a matrix. However, the best way to compute
-- at xTx{} or @xxT{} is @code{crossprod(x)} or @code{x %o% x}
--respectively.}
-+ at xTx{} or @xxT{} is @code{crossprod(x)} or @code{x %o% x} respectively.}
-
- @findex crossprod
- The function @code{crossprod()} forms ``crossproducts'', meaning that
-@@ -2103,13 +2119,13 @@
- potentially unstable to compute @code{x <- solve(A) %*% b} instead of
- @code{solve(A,b)}.
-
--The quadratic form @eqn{@strong{x^T A^{-1} x},@ @code{x %*% A^@{-1@} %*%
-+The quadratic form @eqn{@strong{x^T A^{-1} x},@ @code{x %*% A^@{-1@} %*%
- x} @ } which is used in multivariate computations, should be computed by
- something like at footnote{Even better would be to form a matrix square
--root @eqn{B, B} with @eqn{A = BB^T, A = BB'} and find the squared length of the
--solution of @eqn{By = x, By = x}, perhaps using the Cholesky or
--eigendecomposition of @eqn{A, A}.} @code{x %*% solve(A,x)}, rather than
--computing the inverse of @code{A}.
-+root @eqn{B, B} with @eqn{A = BB^T, A = BB'} and find the squared length
-+of the solution of @eqn{By = x, By = x} , perhaps using the Cholesky or
-+eigen decomposition of @eqn{A, A}. } @code{x %*% solve(A,x)}, rather
-+than computing the inverse of @code{A}.
-
- @node Eigenvalues and eigenvectors, Singular value decomposition and determinants, Linear equations and inversion, Matrix facilities
- @subsection Eigenvalues and eigenvectors
-@@ -2728,9 +2744,9 @@
- facilities are simple and their requirements are fairly strict and even
- rather inflexible. There is a clear presumption by the designers of
- @R{} that you will be able to modify your input files using other tools,
--such as file editors or Perl at footnote{Under UNIX, the utilities Sed or
--Awk can be used.} to fit in with the requirements of @R{}. Generally
--this is very simple.
-+such as file editors or Perl at footnote{Under UNIX, the utilities
-+ at command{sed} or at command{awk} can be used.} to fit in with the
-+requirements of @R{}. Generally this is very simple.
-
- If variables are to be held mainly in data frames, as we strongly
- suggest they should be, an entire data frame can be read directly with
-@@ -5340,13 +5356,15 @@
- display a wide variety of statistical graphs and also to build entirely
- new types of graph.
-
--The graphics facilities can be used in both interactive and batch modes, but in
--most cases, interactive use is more productive. Interactive use is also
--easy because at startup time @R{} initiates a graphics @emph{device
--driver} which opens a special @emph{graphics window} for the display of
--interactive graphics. Although this is done automatically, it is useful
--to know that the command used is @code{X11()} under UNIX,
-- at code{windows()} under Windows and @code{quartz()} under OS X.
-+The graphics facilities can be used in both interactive and batch modes,
-+but in most cases, interactive use is more productive. Interactive use
-+is also easy because at startup time @R{} initiates a graphics
-+ at emph{device driver} which opens a special @emph{graphics window} for
-+the display of interactive graphics. Although this is done
-+automatically, it may useful to know that the command used is
-+ at code{X11()} under UNIX, @code{windows()} under Windows and
-+ at code{quartz()} under OS X. A new device can always be opened by
-+ at code{dev.new()}.
-
- Once the device driver is running, @R{} plotting commands can be used to
- produce a variety of graphical displays and to create entirely new kinds
-diff -ruN R-3.0.1/share/licenses/license.db R-patched/share/licenses/license.db
---- share/licenses/license.db 2013-03-22 19:05:06.000000000 -0400
-+++ share/licenses/license.db 2013-05-24 18:05:06.000000000 -0400
-@@ -128,7 +128,7 @@
- Abbrev: BSD_2_clause
- OSI: open (http://opensource.org/licenses/BSD-2-Clause)
- FSF: free_and_GPLv3_compatible (http://www.gnu.org/licenses/license-list.html#FreeBSD)
--File: src/licenses/BSD_2_clause
-+File: share/licenses/BSD_2_clause
- URL: http://opensource.org/licenses/BSD-2-Clause
- FOSS: yes
- Extensible: yes
-@@ -138,7 +138,7 @@
- Abbrev: BSD_3_clause
- OSI: open (http://opensource.org/licenses/BSD-2-Clause)
- FSF: free_and_GPLv3_compatible (http://www.gnu.org/licenses/license-list.html#ModifiedBSD)
--File: src/licenses/BSD_3_clause
-+File: share/licenses/BSD_3_clause
- URL: http://opensource.org/licenses/BSD-3-Clause
- FOSS: yes
- Extensible: yes
-diff -ruN R-3.0.1/src/include/Rdefines.h R-patched/src/include/Rdefines.h
---- src/include/Rdefines.h 2012-04-15 18:05:02.000000000 -0400
-+++ src/include/Rdefines.h 2013-05-26 18:05:04.000000000 -0400
-@@ -1,6 +1,6 @@
- /*
- * R : A Computer Language for Statistical Data Analysis
-- * Copyright (C) 1999-2007 The R Core Team.
-+ * Copyright (C) 1999-2013 The R Core Team.
- *
- * This program is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
-@@ -133,6 +133,7 @@
- #define SET_DIMNAMES(x, n) setAttrib(x, R_DimNamesSymbol, n)
- #define SET_LEVELS(x, l) setAttrib(x, R_LevelsSymbol, l)
- #define SET_NAMES(x, n) setAttrib(x, R_NamesSymbol, n)
-+/* These do not support long vectors */
- #define GET_LENGTH(x) length(x)
- #define SET_LENGTH(x, n) (x = lengthgets(x, n))
-
-@@ -146,11 +147,25 @@
-
- #define s_object SEXPREC
- #define S_EVALUATOR /**/
--#ifndef TRUE
--#define TRUE 1
--#endif
--#ifndef FALSE
--#define FALSE 0
-+
-+/* These conflict with definitions in R_ext/Boolean.h,
-+ but spatstat relies on them in a C file */
-+#ifdef __cplusplus
-+# ifndef R_EXT_BOOLEAN_H_
-+# ifndef TRUE
-+# define TRUE 1
-+# endif
-+# ifndef FALSE
-+# define FALSE 0
-+# endif
-+# endif
-+#else
-+# ifndef TRUE
-+# define TRUE 1
-+# endif
-+# ifndef FALSE
-+# define FALSE 0
-+# endif
- #endif
-
- #define COPY_TO_USER_STRING(x) mkChar(x)
-Files R-3.0.1/src/library/Recommended/foreign.tgz and R-patched/src/library/Recommended/foreign.tgz differ
-Files R-3.0.1/src/library/Recommended/foreign_0.8-53.tar.gz and R-patched/src/library/Recommended/foreign_0.8-53.tar.gz differ
-Files R-3.0.1/src/library/Recommended/foreign_0.8-54.tar.gz and R-patched/src/library/Recommended/foreign_0.8-54.tar.gz differ
-Files R-3.0.1/src/library/Recommended/mgcv.tgz and R-patched/src/library/Recommended/mgcv.tgz differ
-Files R-3.0.1/src/library/Recommended/mgcv_1.7-22.tar.gz and R-patched/src/library/Recommended/mgcv_1.7-22.tar.gz differ
-Files R-3.0.1/src/library/Recommended/mgcv_1.7-23.tar.gz and R-patched/src/library/Recommended/mgcv_1.7-23.tar.gz differ
-diff -ruN R-3.0.1/src/library/base/R/grep.R R-patched/src/library/base/R/grep.R
---- src/library/base/R/grep.R 2013-03-05 18:02:33.000000000 -0500
-+++ src/library/base/R/grep.R 2013-05-16 18:05:04.000000000 -0400
-@@ -302,6 +302,7 @@
- stop("must have replacement values for matches")
- value <- rep_len(value, np)
- }
-+ y <- y[pos]
- x[pos] <- paste0(sapply(y, `[`, 1L), value, sapply(y, `[`, 2L))
- return(x)
- }
-diff -ruN R-3.0.1/src/library/base/man/sort.Rd R-patched/src/library/base/man/sort.Rd
---- src/library/base/man/sort.Rd 2013-03-05 18:02:35.000000000 -0500
-+++ src/library/base/man/sort.Rd 2013-05-24 18:05:05.000000000 -0400
-@@ -72,7 +72,7 @@
- are more than 10.) Names are discarded for partial sorting.
-
- Method \code{"shell"} uses Shellsort (an \eqn{O(n^{4/3})} variant from
-- Sedgewick (1996)). If \code{x} has names a stable modification is
-+ Sedgewick (1986)). If \code{x} has names a stable modification is
- used, so ties are not reordered. (This only matters if names are
- present.)
-
-diff -ruN R-3.0.1/src/library/grDevices/man/Japanese.Rd R-patched/src/library/grDevices/man/Japanese.Rd
---- src/library/grDevices/man/Japanese.Rd 2012-12-05 09:37:58.000000000 -0500
-+++ src/library/grDevices/man/Japanese.Rd 2013-05-16 18:05:04.000000000 -0400
-@@ -37,8 +37,8 @@
- par(cex = 3)
- Vf <- c("serif", "plain")
- % doubled "\" -> can't execute here!
--text(4, 2, "\\\\#J2438\\\\#J2421\\\\#J2451\\\\#J2473", vfont = Vf)
--text(4, 4, "\\\\#J2538\\\\#J2521\\\\#J2551\\\\#J2573", vfont = Vf)
-+text(4, 2, "\\\\#J244b\\\\#J245b\\\\#J2473", vfont = Vf)
-+text(4, 4, "\\\\#J2538\\\\#J2563\\\\#J2551\\\\#J2573", vfont = Vf)
- text(4, 6, "\\\\#J467c\\\\#J4b5c", vfont = Vf)
- text(4, 8, "Japan", vfont = Vf)
- par(cex = 1)
-diff -ruN R-3.0.1/src/library/graphics/man/par.Rd R-patched/src/library/graphics/man/par.Rd
---- src/library/graphics/man/par.Rd 2013-03-05 18:02:29.000000000 -0500
-+++ src/library/graphics/man/par.Rd 2013-05-24 18:05:04.000000000 -0400
-@@ -729,10 +729,12 @@
- plot(0:1, 0:1, type = "n", axes = FALSE, ann = FALSE)
- y <- (n:1)/(n+1)
- clty <- as.character(ltys)
-- mytext <- function(x,y, txt) text(x, y, txt, adj = c(0, -.3), cex = 0.8, ...)
-+ mytext <- function(x, y, txt)
-+ text(x, y, txt, adj = c(0, -.3), cex = 0.8, ...)
- abline(h = y, lty = ltys, ...); mytext(xoff, y, clty)
- y <- y - 1/(3*(n+1))
-- abline(h = y, lty = ltys, lwd = 2, ...); mytext(1/8+xoff, y, paste(clty," lwd = 2"))
-+ abline(h = y, lty = ltys, lwd = 2, ...)
-+ mytext(1/8+xoff, y, paste(clty," lwd = 2"))
- }
- showLty(c("solid", "dashed", "dotted", "dotdash", "longdash", "twodash"))
- par(new = TRUE) # the same:
-Files R-3.0.1/src/library/grid/inst/doc/displaylist.pdf and R-patched/src/library/grid/inst/doc/displaylist.pdf differ
-Files R-3.0.1/src/library/grid/inst/doc/frame.pdf and R-patched/src/library/grid/inst/doc/frame.pdf differ
-Files R-3.0.1/src/library/grid/inst/doc/grid.pdf and R-patched/src/library/grid/inst/doc/grid.pdf differ
-Files R-3.0.1/src/library/grid/inst/doc/grobs.pdf and R-patched/src/library/grid/inst/doc/grobs.pdf differ
-Files R-3.0.1/src/library/grid/inst/doc/interactive.pdf and R-patched/src/library/grid/inst/doc/interactive.pdf differ
-Files R-3.0.1/src/library/grid/inst/doc/locndimn.pdf and R-patched/src/library/grid/inst/doc/locndimn.pdf differ
-Files R-3.0.1/src/library/grid/inst/doc/moveline.pdf and R-patched/src/library/grid/inst/doc/moveline.pdf differ
-Files R-3.0.1/src/library/grid/inst/doc/nonfinite.pdf and R-patched/src/library/grid/inst/doc/nonfinite.pdf differ
-Files R-3.0.1/src/library/grid/inst/doc/plotexample.pdf and R-patched/src/library/grid/inst/doc/plotexample.pdf differ
-Files R-3.0.1/src/library/grid/inst/doc/rotated.pdf and R-patched/src/library/grid/inst/doc/rotated.pdf differ
-Files R-3.0.1/src/library/grid/inst/doc/saveload.pdf and R-patched/src/library/grid/inst/doc/saveload.pdf differ
-Files R-3.0.1/src/library/grid/inst/doc/sharing.pdf and R-patched/src/library/grid/inst/doc/sharing.pdf differ
-Files R-3.0.1/src/library/grid/inst/doc/viewports.pdf and R-patched/src/library/grid/inst/doc/viewports.pdf differ
-diff -ruN R-3.0.1/src/library/methods/man/representation.Rd R-patched/src/library/methods/man/representation.Rd
---- src/library/methods/man/representation.Rd 2013-03-05 18:02:31.000000000 -0500
-+++ src/library/methods/man/representation.Rd 2013-05-16 18:05:04.000000000 -0400
-@@ -8,13 +8,15 @@
- \alias{prototype}
- \title{ Construct a Representation or a Prototype for a Class Definition}
- \description{
-- In calls to
-- \code{\link{setClass}}, these two functions construct,
-- respectively, the \code{representation} and \code{prototype}
-- arguments. They do various checks and handle special cases. You're
-- encouraged to use them when defining classes that, for
-- example, extend other classes as a data part or have multiple
-- superclasses, or that combine extending a class and slots.
-+ These are old utility functions to construct, respectively
-+ a list designed to represent the slots and superclasses and
-+ a list of prototype specifications. The \code{representation()}
-+ function is no longer useful, since the arguments \code{slots} and
-+ \code{contains} to \code{\link{setClass}} are now recommended.
-+
-+ The \code{prototype()} function may still be used for the
-+ corresponding argument, but a
-+ simple list of the same arguments works as well.
- }
- \usage{
- representation(...)
-diff -ruN R-3.0.1/src/library/methods/man/setClass.Rd R-patched/src/library/methods/man/setClass.Rd
---- src/library/methods/man/setClass.Rd 2013-03-05 18:02:31.000000000 -0500
-+++ src/library/methods/man/setClass.Rd 2013-05-16 18:05:04.000000000 -0400
-@@ -15,7 +15,7 @@
- is returned as the value of \code{setClass()}, suitable for creating
- objects from the class if the class is not virtual. Of the many
- arguments to the function only \code{Class},
-- \code{representation} and \code{contains} are usually needed.
-+ \code{slots=} and \code{contains=} are usually needed.
- }
- \usage{
- setClass(Class, representation, prototype, contains=character(),
-diff -ruN R-3.0.1/src/library/methods/src/slot.c R-patched/src/library/methods/src/slot.c
---- src/library/methods/src/slot.c 2012-04-15 18:05:17.000000000 -0400
-+++ src/library/methods/src/slot.c 2013-05-25 18:05:04.000000000 -0400
-@@ -1,6 +1,6 @@
- /*
- * R : A Computer Language for Statistical Data Analysis
-- * Copyright (C) 2001-2005 The R Core Team.
-+ * Copyright (C) 2001-2013 The R Core Team.
- *
- * This program is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
-@@ -18,7 +18,6 @@
- */
-
- #include <R.h>
--#include <Rdefines.h>
- #include <Rinternals.h>
- #include "methods.h"
-
-Files R-3.0.1/src/library/parallel/inst/doc/parallel.pdf and R-patched/src/library/parallel/inst/doc/parallel.pdf differ
-diff -ruN R-3.0.1/src/library/stats/R/median.R R-patched/src/library/stats/R/median.R
---- src/library/stats/R/median.R 2012-08-05 18:05:06.000000000 -0400
-+++ src/library/stats/R/median.R 2013-05-24 18:05:04.000000000 -0400
-@@ -21,8 +21,9 @@
- median.default <- function(x, na.rm = FALSE)
- {
- if(is.factor(x) || is.data.frame(x)) stop("need numeric data")
-- ## all other objects only need sort() & mean() to be working
-+ ## all other objects only need is.na(), sort() & mean() to be working
- if(length(names(x))) names(x) <- NULL # for e.g., c(x = NA_real_)
-+## if(na.rm) x <- x[!is.na(x)] else if(anyNA(x)) return(x[FALSE][NA])
- if(na.rm) x <- x[!is.na(x)] else if(any(is.na(x))) return(x[FALSE][NA])
- n <- length(x)
- if (n == 0L) return(x[FALSE][NA])
-diff -ruN R-3.0.1/src/library/stats/man/median.Rd R-patched/src/library/stats/man/median.Rd
---- src/library/stats/man/median.Rd 2013-03-05 18:02:25.000000000 -0500
-+++ src/library/stats/man/median.Rd 2013-05-24 18:05:04.000000000 -0400
-@@ -21,10 +21,11 @@
- }
- \details{
- This is a generic function for which methods can be written. However,
-- the default method makes use of \code{sort} and \code{mean} from
-- package \pkg{base} both of which are generic, and so the default
-- method will work for most classes (e.g. \code{"\link{Date}"}) for
-- which a median is a reasonable concept.
-+ the default method makes use of \code{is.na}, \code{sort} and
-+ \code{mean} from package \pkg{base} all of which are generic, and so
-+ the default method will work for most classes
-+ (e.g. \code{"\link{Date}"}) for which a median is a reasonable
-+ concept.
- }
- \value{
- The default method returns a length-one object of the same type as
-diff -ruN R-3.0.1/src/library/stats/src/distance.c R-patched/src/library/stats/src/distance.c
---- src/library/stats/src/distance.c 2013-03-05 18:02:24.000000000 -0500
-+++ src/library/stats/src/distance.c 2013-05-24 18:05:04.000000000 -0400
-@@ -29,7 +29,7 @@
- #include <Rmath.h>
- #include <float.h>
- #include "stats.h"
--#ifdef HAVE_OPENMP
-+#ifdef _OPENMP
- # include <R_ext/MathThreads.h>
- #endif
-
-@@ -201,7 +201,7 @@
- int dc, i, j;
- size_t ij; /* can exceed 2^31 - 1 */
- double (*distfun)(double*, int, int, int, int) = NULL;
--#ifdef HAVE_OPENMP
-+#ifdef _OPENMP
- int nthreads;
- #endif
-
-@@ -229,7 +229,7 @@
- error(_("distance(): invalid distance"));
- }
- dc = (*diag) ? 0 : 1; /* diag=1: we do the diagonal */
--#ifdef HAVE_OPENMP
-+#ifdef _OPENMP
- if (R_num_math_threads > 0)
- nthreads = R_num_math_threads;
- else
-diff -ruN R-3.0.1/src/library/tools/R/Rd2ex.R R-patched/src/library/tools/R/Rd2ex.R
---- src/library/tools/R/Rd2ex.R 2012-08-05 18:05:08.000000000 -0400
-+++ src/library/tools/R/Rd2ex.R 2013-05-25 18:05:03.000000000 -0400
-@@ -20,7 +20,7 @@
-
- Rd2ex <-
- function(Rd, out="", defines=.Platform$OS.type, stages="render",
-- outputEncoding="UTF-8", ...)
-+ outputEncoding="UTF-8", commentDontrun = TRUE, ...)
- {
- encode_warn <- FALSE
- WriteLines <- function(x, con, outputEncoding, ...) {
-@@ -73,21 +73,22 @@
- writeLines("", con)
- of1("## End Don't show")
- } else if (tag == "\\dontrun") {
-- ## Special case for one line.
-- if (length(x) == 1L) {
-+ if (commentDontrun)
- of1("## Not run: ")
-+ ## Special case for one line.
-+ if (length(x) == 1L && commentDontrun) {
- render(x[[1L]], prefix)
- } else {
-- of1("## Not run: ")
- if (!grepl("^\n", x[[1L]][1L], perl = TRUE) && RdTags(x)[1L] != "COMMENT") {
- writeLines("", con)
-- render(x[[1L]], paste("##D", prefix))
-+ render(x[[1L]], paste0(if (commentDontrun) "##D ", prefix))
- } else render(x[[1L]], prefix)
-- for(i in 2:length(x)) render(x[[i]], paste("##D", prefix))
-+ for(i in 2:length(x)) render(x[[i]], paste0(if (commentDontrun) "##D ", prefix))
- last <- x[[length(x)]]
- if (!grepl("\n$", last[length(last)], perl = TRUE))
- writeLines("", con)
-- of1("## End(Not run)")
-+ if (commentDontrun)
-+ of1("## End(Not run)")
- }
- } else if (tag == "\\donttest") {
- of1("## No test: ")
-diff -ruN R-3.0.1/src/library/tools/R/check.R R-patched/src/library/tools/R/check.R
---- src/library/tools/R/check.R 2013-04-22 18:05:03.000000000 -0400
-+++ src/library/tools/R/check.R 2013-05-20 18:05:04.000000000 -0400
-@@ -3313,9 +3313,10 @@
- " -v, --version print version info and exit",
- " -l, --library=LIB library directory used for test installation",
- " of packages (default is outdir)",
-- " -o, --outdir=DIR directory used for logfiles, R output, etc.",
-- " (default is 'pkg.Rcheck' in current directory,",
-- " where 'pkg' is the name of the package checked)",
-+ " -o, --output=DIR directory for output, default is current directory.",
-+ " Logfiles, R output, etc. will be placed in 'pkg.Rcheck'",
-+ " in this directory, where 'pkg' is the name of the",
-+ " checked package",
- " --no-clean do not clean 'outdir' before using it",
- " --no-codoc do not check for code/documentation mismatches",
- " --no-examples do not run the examples in the Rd files",
-diff -ruN R-3.0.1/src/library/tools/man/Rd2HTML.Rd R-patched/src/library/tools/man/Rd2HTML.Rd
---- src/library/tools/man/Rd2HTML.Rd 2013-03-05 18:02:28.000000000 -0500
-+++ src/library/tools/man/Rd2HTML.Rd 2013-05-25 18:05:03.000000000 -0400
-@@ -30,7 +30,8 @@
- fragment = FALSE, ..., writeEncoding = TRUE)
-
- Rd2ex(Rd, out = "", defines = .Platform$OS.type,
-- stages = "render", outputEncoding = "UTF-8", ...)
-+ stages = "render", outputEncoding = "UTF-8",
-+ commentDontrun = TRUE, ...)
- }
- \arguments{
- \item{Rd}{ a filename or \code{Rd} object to use as input. }
-@@ -57,6 +58,8 @@
- \code{Rd} is a filename. }
- \item{writeEncoding}{should \verb{\inputencoding} lines be written in
- the file for non-ASCII encodings?}
-+ \item{commentDontrun}{should \verb{\dontrun} sections be commented
-+ out?}
- }
- \details{
- These functions convert help documents: \code{Rd2HTML} produces HTML,
-diff -ruN R-3.0.1/src/library/tools/src/Makefile.in R-patched/src/library/tools/src/Makefile.in
---- src/library/tools/src/Makefile.in 2013-03-05 18:02:28.000000000 -0500
-+++ src/library/tools/src/Makefile.in 2013-05-16 07:42:08.000000000 -0400
-@@ -64,6 +64,6 @@
- $(srcdir)/gramLatex.c: @MAINTAINER_MODE_TRUE@ $(srcdir)/gramLatex.y
- @$(ECHO) "re-making gramLatex.c"
- $(YACC) $(YFLAGS) $(srcdir)/gramLatex.y
-- $(SHELL) $(top_srcdir)/tools/move-if-change y.tab.c $(srcdir)/gramLatex.
-+ $(SHELL) $(top_srcdir)/tools/move-if-change y.tab.c $(srcdir)/gramLatex.c
-
- ## Automagically generated dependencies:
-diff -ruN R-3.0.1/src/library/utils/R/example.R R-patched/src/library/utils/R/example.R
---- src/library/utils/R/example.R 2012-08-05 18:05:07.000000000 -0400
-+++ src/library/utils/R/example.R 2013-05-25 18:05:03.000000000 -0400
-@@ -22,7 +22,8 @@
- character.only = FALSE, give.lines = FALSE, local = FALSE,
- echo = TRUE, verbose = getOption("verbose"), setRNG = FALSE,
- ask = getOption("example.ask"),
-- prompt.prefix = abbreviate(topic, 6))
-+ prompt.prefix = abbreviate(topic, 6),
-+ run.dontrun = FALSE)
- {
- if (!character.only) {
- topic <- substitute(topic)
-@@ -39,7 +40,7 @@
- pkgname <- basename(packagePath)
- lib <- dirname(packagePath)
- tf <- tempfile("Rex")
-- tools::Rd2ex(.getHelpFile(file), tf)
-+ tools::Rd2ex(.getHelpFile(file), tf, commentDontrun = !run.dontrun)
- if (!file.exists(tf)) {
- if(give.lines) return(character())
- warning(gettextf("%s has a help file but no examples", sQuote(topic)),
-diff -ruN R-3.0.1/src/library/utils/R/help.request.R R-patched/src/library/utils/R/help.request.R
---- src/library/utils/R/help.request.R 2013-03-05 18:02:26.000000000 -0500
-+++ src/library/utils/R/help.request.R 2013-05-16 18:05:04.000000000 -0400
-@@ -1,7 +1,7 @@
- # File src/library/utils/R/unix/help.request.R
- # Part of the R package, http://www.R-project.org
- #
--# Copyright (C) 1995-2012 The R Core Team
-+# Copyright (C) 1995-2013 The R Core Team
- #
- # This program is free software; you can redistribute it and/or modify
- # it under the terms of the GNU General Public License as published by
-@@ -95,10 +95,9 @@
- if(no(other)) return("Please do this first.")
- }
-
-- man <- url("http://cran.r-project.org/manuals.html")
-- ver <- scan(man, what = character(0L), sep = "\n", skip = 13L, nlines = 1L,
-- quiet = TRUE)
-- ver <- strsplit(ver, " ")[[1L]][3L]
-+ page <- url("http://cran.r-project.org/bin/windows/base")
-+ title <- grep("<title>", readLines(page, 10L), fixed = TRUE, value = TRUE)
-+ ver <- sub("^.*R-([^ ]*) for Windows.*$", "\\1", title)
- if (getRversion() < numeric_version(ver)) {
- update <- readMyLine("Your R version is out-of-date,",
- "would you like to update now?")
-Files R-3.0.1/src/library/utils/inst/doc/Sweave.pdf and R-patched/src/library/utils/inst/doc/Sweave.pdf differ
-diff -ruN R-3.0.1/src/library/utils/man/example.Rd R-patched/src/library/utils/man/example.Rd
---- src/library/utils/man/example.Rd 2012-12-05 09:37:55.000000000 -0500
-+++ src/library/utils/man/example.Rd 2013-05-25 18:05:03.000000000 -0400
-@@ -16,7 +16,8 @@
- character.only = FALSE, give.lines = FALSE, local = FALSE,
- echo = TRUE, verbose = getOption("verbose"),
- setRNG = FALSE, ask = getOption("example.ask"),
-- prompt.prefix = abbreviate(topic, 6))
-+ prompt.prefix = abbreviate(topic, 6),
-+ run.dontrun = FALSE)
- }
- \arguments{
- \item{topic}{name or literal character string: the online
-@@ -53,6 +54,8 @@
- device and to any devices opened by the example code.}
- \item{prompt.prefix}{character; prefixes the prompt to be used if
- \code{echo = TRUE}.}
-+ \item{run.dontrun}{logical indicating that \verb{\dontrun}
-+ should be ignored.}
- }
- \value{
- The value of the last evaluated expression, unless \code{give.lines}
-diff -ruN R-3.0.1/src/main/RNG.c R-patched/src/main/RNG.c
---- src/main/RNG.c 2013-03-18 19:05:08.000000000 -0400
-+++ src/main/RNG.c 2013-05-24 18:05:05.000000000 -0400
-@@ -441,7 +441,7 @@
- /* Choose a new kind of RNG.
- * Initialize its seed by calling the old RNG's unif_rand()
- */
-- if (newkind == -1) newkind = RNG_DEFAULT;
-+ if (newkind == (RNGtype)-1) newkind = RNG_DEFAULT;
- switch(newkind) {
- case WICHMANN_HILL:
- case MARSAGLIA_MULTICARRY:
-@@ -465,7 +465,7 @@
- {
- /* N01type is an enumeration type, so this will probably get
- mapped to an unsigned integer type. */
-- if (kind == -1) kind = N01_DEFAULT;
-+ if (kind == (N01type)-1) kind = N01_DEFAULT;
- if (kind > KINDERMAN_RAMAGE)
- error(_("invalid Normal type in 'RNGkind'"));
- if (kind == USER_NORM) {
-diff -ruN R-3.0.1/src/main/array.c R-patched/src/main/array.c
---- src/main/array.c 2013-04-19 18:05:04.000000000 -0400
-+++ src/main/array.c 2013-05-24 18:05:05.000000000 -0400
-@@ -1267,7 +1267,7 @@
-
- if (OP == 0 || OP == 1) { /* columns */
- PROTECT(ans = allocVector(REALSXP, p));
--#ifdef HAVE_OPENMP
-+#ifdef _OPENMP
- int nthreads;
- /* This gives a spurious -Wunused-but-set-variable error */
- if (R_num_math_threads > 0)
-diff -ruN R-3.0.1/src/main/platform.c R-patched/src/main/platform.c
---- src/main/platform.c 2013-04-15 18:05:05.000000000 -0400
-+++ src/main/platform.c 2013-05-16 18:05:04.000000000 -0400
-@@ -830,10 +830,16 @@
- for (i = 0; i < n; i++) {
- #ifdef Win32
- wchar_t *wfn = filenameToWchar(STRING_ELT(fn, i), TRUE);
-- /* 'Sharpie' and fellow ignorami use trailing / on Windows,
-- where it is not valid */
-- wchar_t *p = wfn + (wcslen(wfn) - 1);
-- if (*p == L'/' || *p == L'\\') *p = 0;
-+ /* trailing \ is not valid on Windows except for the
-+ root directory on a drive, specified as "\", or "D:\",
-+ or "\\?\D:\", etc. We remove it in other cases,
-+ to help those who think they're on Unix. */
-+ size_t len = wcslen(wfn);
-+ if (len) {
-+ wchar_t *p = wfn + (len - 1);
-+ if (len > 1 && (*p == L'/' || *p == L'\\') &&
-+ *(p-1) != L':') *p = 0;
-+ }
- #else
- const char *efn = R_ExpandFileName(translateChar(STRING_ELT(fn, i)));
- #endif
-diff -ruN R-3.0.1/src/scripts/config R-patched/src/scripts/config
---- src/scripts/config 2013-04-18 18:05:05.000000000 -0400
-+++ src/scripts/config 2013-05-18 18:05:03.000000000 -0400
-@@ -20,7 +20,7 @@
- ## A copy of the GNU General Public License is available at
- ## http://www.r-project.org/Licenses/
-
--revision='$Revision: 1.1 $'
-+revision='$Revision: 1.1 $'
- version=`set - ${revision}; echo ${2}`
- version="R configuration information retrieval script: ${R_VERSION} (r${version})
-
-@@ -219,7 +219,7 @@
- makefiles="${makefiles} -f ${HOME}/.R/Makevars"
- fi
- else
-- . ${R_HOME}/etc/Renviron
-+ . ${R_HOME}/etc${R_ARCH}/Renviron
- if test -n "${R_MAKEVARS_USER}"; then
- makefiles="${makefiles} -f ${R_MAKEVARS_USER}"
- elif test -f "${HOME}/.R/Makevars-${R_PLATFORM}"; then
-diff -ruN R-3.0.1/tests/Examples/datasets-Ex.Rout.save R-patched/tests/Examples/datasets-Ex.Rout.save
---- tests/Examples/datasets-Ex.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/Examples/datasets-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-@@ -3434,8 +3434,9 @@
- >
- > ### * <FOOTER>
- > ###
-+> options(digits = 7L)
- > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
--Time elapsed: 1.83 0.038 1.874 0 0
-+Time elapsed: 1.864 0.034 1.905 0 0
- > grDevices::dev.off()
- null device
- 1
-diff -ruN R-3.0.1/tests/Examples/grDevices-Ex.Rout.save R-patched/tests/Examples/grDevices-Ex.Rout.save
---- tests/Examples/grDevices-Ex.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/Examples/grDevices-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-@@ -115,8 +115,8 @@
- + main = "example(Japanese)", xlab = "using Hershey fonts")
- > par(cex = 3)
- > Vf <- c("serif", "plain")
--> text(4, 2, "\\#J2438\\#J2421\\#J2451\\#J2473", vfont = Vf)
--> text(4, 4, "\\#J2538\\#J2521\\#J2551\\#J2573", vfont = Vf)
-+> text(4, 2, "\\#J244b\\#J245b\\#J2473", vfont = Vf)
-+> text(4, 4, "\\#J2538\\#J2563\\#J2551\\#J2573", vfont = Vf)
- > text(4, 6, "\\#J467c\\#J4b5c", vfont = Vf)
- > text(4, 8, "Japan", vfont = Vf)
- > par(cex = 1)
-@@ -3705,8 +3705,9 @@
- >
- > ### * <FOOTER>
- > ###
-+> options(digits = 7L)
- > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
--Time elapsed: 8.757 0.186 8.972 0 0
-+Time elapsed: 8.732 0.198 8.968 0 0
- > grDevices::dev.off()
- null device
- 1
-diff -ruN R-3.0.1/tests/Examples/graphics-Ex.Rout.save R-patched/tests/Examples/graphics-Ex.Rout.save
---- tests/Examples/graphics-Ex.Rout.save 2013-05-02 18:05:04.000000000 -0400
-+++ tests/Examples/graphics-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 Patched (2013-05-01 r62701) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-@@ -1622,10 +1622,12 @@
- + plot(0:1, 0:1, type = "n", axes = FALSE, ann = FALSE)
- + y <- (n:1)/(n+1)
- + clty <- as.character(ltys)
--+ mytext <- function(x,y, txt) text(x, y, txt, adj = c(0, -.3), cex = 0.8, ...)
-++ mytext <- function(x, y, txt)
-++ text(x, y, txt, adj = c(0, -.3), cex = 0.8, ...)
- + abline(h = y, lty = ltys, ...); mytext(xoff, y, clty)
- + y <- y - 1/(3*(n+1))
--+ abline(h = y, lty = ltys, lwd = 2, ...); mytext(1/8+xoff, y, paste(clty," lwd = 2"))
-++ abline(h = y, lty = ltys, lwd = 2, ...)
-++ mytext(1/8+xoff, y, paste(clty," lwd = 2"))
- + }
- > showLty(c("solid", "dashed", "dotted", "dotdash", "longdash", "twodash"))
- > par(new = TRUE) # the same:
-@@ -2025,7 +2027,7 @@
- > points.default # to see how it calls "plot.xy(xy.coords(x, y), ...)"
- function (x, y = NULL, type = "p", ...)
- plot.xy(xy.coords(x, y), type = type, ...)
--<bytecode: 0x3f8a6b8>
-+<bytecode: 0x3b03758>
- <environment: namespace:graphics>
- >
- >
-@@ -2925,7 +2927,7 @@
- u <- par("usr")
- xy * c(u[2L] - u[1L], u[4L] - u[3L])/par("pin")
- }
--<bytecode: 0x4773828>
-+<bytecode: 0x4755578>
- <environment: namespace:graphics>
- >
- > ## plot labels offset 0.12 inches to the right
-@@ -3005,7 +3007,7 @@
- > ###
- > options(digits = 7L)
- > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
--Time elapsed: 7.676 0.165 7.975 0 0
-+Time elapsed: 3.625 0.055 3.69 0 0
- > grDevices::dev.off()
- null device
- 1
-diff -ruN R-3.0.1/tests/Examples/grid-Ex.Rout.save R-patched/tests/Examples/grid-Ex.Rout.save
---- tests/Examples/grid-Ex.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/Examples/grid-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-@@ -1960,8 +1960,9 @@
- >
- > ### * <FOOTER>
- > ###
-+> options(digits = 7L)
- > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
--Time elapsed: 1.44 0.026 1.472 0 0
-+Time elapsed: 1.393 0.019 1.417 0 0
- > grDevices::dev.off()
- null device
- 1
-diff -ruN R-3.0.1/tests/Examples/splines-Ex.Rout.save R-patched/tests/Examples/splines-Ex.Rout.save
---- tests/Examples/splines-Ex.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/Examples/splines-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-@@ -612,8 +612,9 @@
- >
- > ### * <FOOTER>
- > ###
-+> options(digits = 7L)
- > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
--Time elapsed: 1.443 0.013 1.462 0 0
-+Time elapsed: 1.422 0.023 1.451 0 0
- > grDevices::dev.off()
- null device
- 1
-diff -ruN R-3.0.1/tests/Examples/stats-Ex.Rout.save R-patched/tests/Examples/stats-Ex.Rout.save
---- tests/Examples/stats-Ex.Rout.save 2013-04-04 18:05:03.000000000 -0400
-+++ tests/Examples/stats-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 Patched (2013-04-04 r62492) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-@@ -3713,7 +3713,7 @@
- >
- > asOneSidedFormula("age")
- ~age
--<environment: 0x45ca580>
-+<environment: 0x3b883b8>
- > asOneSidedFormula(~ age)
- ~age
- >
-@@ -4714,7 +4714,7 @@
- r[cbind(1L:p, 1L:p)] <- 1
- r
- }
--<bytecode: 0x7542ac8>
-+<bytecode: 0x7166e98>
- <environment: namespace:stats>
- > stopifnot(all.equal(Cl, cov2cor(cov(longley))),
- + all.equal(cor(longley, method = "kendall"),
-@@ -6731,8 +6731,8 @@
- > gf$linkinv
- function (eta)
- 1/eta
--<bytecode: 0x49b50a8>
--<environment: 0x9e6a100>
-+<bytecode: 0x3b63990>
-+<environment: 0x89f5328>
- > gf$variance(-3:4) #- == (.)^2
- [1] 9 4 1 0 1 4 9 16
- >
-@@ -7133,7 +7133,7 @@
- > environment(as.formula("y ~ x"))
- <environment: R_GlobalEnv>
- > environment(as.formula("y ~ x", env = new.env()))
--<environment: 0xa03f7b0>
-+<environment: 0x8ad7090>
- >
- >
- > ## Create a formula for a model with a large number of variables:
-@@ -11709,26 +11709,26 @@
- $linkfun
- function (mu)
- mu
--<bytecode: 0x49b2298>
--<environment: 0x97631a8>
-+<bytecode: 0x3b61340>
-+<environment: 0xa483b80>
-
- $linkinv
- function (eta)
- eta
--<bytecode: 0x49b2228>
--<environment: 0x97631a8>
-+<bytecode: 0x3b612d0>
-+<environment: 0xa483b80>
-
- $mu.eta
- function (eta)
- rep.int(1, length(eta))
--<bytecode: 0x49b21b8>
--<environment: 0x97631a8>
-+<bytecode: 0x3b61260>
-+<environment: 0xa483b80>
-
- $valideta
- function (eta)
- TRUE
--<bytecode: 0x49b1ff8>
--<environment: 0x97631a8>
-+<bytecode: 0x3b610a0>
-+<environment: 0xa483b80>
-
- $name
- [1] "identity"
-@@ -11739,14 +11739,14 @@
- $linkfun
- function (mu)
- mu^lambda
--<bytecode: 0x9b36060>
--<environment: 0x9cff078>
-+<bytecode: 0xa485138>
-+<environment: 0xa431038>
-
- $linkinv
- function (eta)
- pmax(eta^(1/lambda), .Machine$double.eps)
--<bytecode: 0x9ae7638>
--<environment: 0x9cff078>
-+<bytecode: 0xa485288>
-+<environment: 0xa431038>
-
- >
- >
-@@ -15540,8 +15540,8 @@
- > unclass(sfun0)
- function (v)
- .approxfun(x, y, v, method, yleft, yright, f)
--<bytecode: 0x4486820>
--<environment: 0x9b6c3f0>
-+<bytecode: 0x3d223d0>
-+<environment: 0x9ecb258>
- attr(,"call")
- stepfun(1:3, y0, f = 0)
- > ls(envir = environment(sfun0))
-@@ -17793,7 +17793,7 @@
- > ###
- > options(digits = 7L)
- > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
--Time elapsed: 14.992 0.275 15.886 0 0
-+Time elapsed: 7.265 0.173 7.469 0 0
- > grDevices::dev.off()
- null device
- 1
-diff -ruN R-3.0.1/tests/Examples/stats4-Ex.Rout.save R-patched/tests/Examples/stats4-Ex.Rout.save
---- tests/Examples/stats4-Ex.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/Examples/stats4-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-@@ -182,8 +182,9 @@
- >
- > ### * <FOOTER>
- > ###
-+> options(digits = 7L)
- > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
--Time elapsed: 0.465 0.004 0.471 0 0
-+Time elapsed: 0.424 0.005 0.431 0 0
- > grDevices::dev.off()
- null device
- 1
-diff -ruN R-3.0.1/tests/Examples/tools-Ex.Rout.save R-patched/tests/Examples/tools-Ex.Rout.save
---- tests/Examples/tools-Ex.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/Examples/tools-Ex.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-@@ -100,7 +100,7 @@
- $enumFormat
- function (n)
- sprintf("%d. ", n)
--<environment: 0x382b150>
-+<environment: 0x2d47fe0>
-
- $showURLs
- [1] FALSE
-@@ -134,7 +134,7 @@
- $enumFormat
- function (n)
- sprintf("%d. ", n)
--<environment: 0x382b150>
-+<environment: 0x2d47fe0>
-
- $showURLs
- [1] FALSE
-@@ -168,7 +168,7 @@
- $enumFormat
- function (n)
- sprintf("%d. ", n)
--<environment: 0x382b150>
-+<environment: 0x2d47fe0>
-
- $showURLs
- [1] FALSE
-@@ -232,7 +232,7 @@
- > bibstyle("unsorted", sortKeys = function(refs) seq_along(refs),
- + fmtPrefix = function(paper) paste0("[", paper$.index, "]"),
- + .init = TRUE)
--<environment: 0x3750a78>
-+<environment: 0x2d29810>
- > print(refs, .bibstyle = "unsorted")
- [1] R Core Team (2013). _R: A Language and Environment for Statistical
- Computing_. R Foundation for Statistical Computing, Vienna, Austria.
-@@ -906,7 +906,7 @@
- > flush(stderr()); flush(stdout())
- >
- > ### Name: vignetteEngine
--> ### Title: Set or get a vignette processing engine.
-+> ### Title: Set or Get a Vignette Processing Engine
- > ### Aliases: vignetteEngine
- > ### Keywords: utilities documentation
- >
-@@ -962,8 +962,9 @@
- >
- > ### * <FOOTER>
- > ###
-+> options(digits = 7L)
- > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
--Time elapsed: 0.311 0.014 0.326 0 0
-+Time elapsed: 0.342 0.007 0.35 0 0
- > grDevices::dev.off()
- null device
- 1
-diff -ruN R-3.0.1/tests/any-all.Rout.save R-patched/tests/any-all.Rout.save
---- tests/any-all.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/any-all.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/arith-true.Rout.save R-patched/tests/arith-true.Rout.save
---- tests/arith-true.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/arith-true.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-@@ -323,5 +323,5 @@
- >
- > ## Last Line:
- > cat('Time elapsed: ', proc.time() - .proctime00,'\n')
--Time elapsed: 0.241 0.002 0.243 0 0
-+Time elapsed: 0.24 0.004 0.245 0 0
- >
-diff -ruN R-3.0.1/tests/arith.Rout.save R-patched/tests/arith.Rout.save
---- tests/arith.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/arith.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/array-subset.Rout.save R-patched/tests/array-subset.Rout.save
---- tests/array-subset.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/array-subset.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/complex.Rout.save R-patched/tests/complex.Rout.save
---- tests/complex.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/complex.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/d-p-q-r-tests.Rout.save R-patched/tests/d-p-q-r-tests.Rout.save
---- tests/d-p-q-r-tests.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/d-p-q-r-tests.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-@@ -1315,5 +1315,5 @@
- >
- >
- > cat("Time elapsed: ", proc.time() - .ptime,"\n")
--Time elapsed: 0.83 0.002 0.835 0 0
-+Time elapsed: 0.847 0.008 0.857 0 0
- >
-diff -ruN R-3.0.1/tests/datasets.Rout.save R-patched/tests/datasets.Rout.save
---- tests/datasets.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/datasets.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/demos.Rout.save R-patched/tests/demos.Rout.save
---- tests/demos.Rout.save 2013-04-26 18:05:04.000000000 -0400
-+++ tests/demos.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -115,8 +115,8 @@
- + "\n\t starting with 'is.' :\t ",
- + sum(grepl("^is\\.", ls.base[base.is.f])), "\n", sep = "")
-
--Number of base objects: 1265
--Number of functions in base: 1223
-+Number of base objects: 1264
-+Number of functions in base: 1222
- starting with 'is.' : 49
-
- > ## 0.14 : 31
-diff -ruN R-3.0.1/tests/eval-etc.Rout.save R-patched/tests/eval-etc.Rout.save
---- tests/eval-etc.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/eval-etc.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/iec60559.Rout.save R-patched/tests/iec60559.Rout.save
---- tests/iec60559.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/iec60559.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/internet.Rout.save R-patched/tests/internet.Rout.save
---- tests/internet.Rout.save 2013-04-03 03:00:03.000000000 -0400
-+++ tests/internet.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-04-02 r62479) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-@@ -29,7 +29,7 @@
- >
- > # test do_download.
- > nrow(available.packages(contrib.url("http://cran.r-project.org")))
--[1] 4407
-+[1] 4538
- >
- > # test url connections on http
- > zz <- url("http://cran.r-project.org/")
-diff -ruN R-3.0.1/tests/lapack.Rout.save R-patched/tests/lapack.Rout.save
---- tests/lapack.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/lapack.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/lm-tests.Rout.save R-patched/tests/lm-tests.Rout.save
---- tests/lm-tests.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/lm-tests.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/method-dispatch.Rout.save R-patched/tests/method-dispatch.Rout.save
---- tests/method-dispatch.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/method-dispatch.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/ok-errors.Rout.save R-patched/tests/ok-errors.Rout.save
---- tests/ok-errors.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/ok-errors.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/print-tests.Rout.save R-patched/tests/print-tests.Rout.save
---- tests/print-tests.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/print-tests.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/reg-IO.Rout.save R-patched/tests/reg-IO.Rout.save
---- tests/reg-IO.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/reg-IO.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/reg-IO2.Rout.save R-patched/tests/reg-IO2.Rout.save
---- tests/reg-IO2.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/reg-IO2.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/reg-S4.Rout.save R-patched/tests/reg-S4.Rout.save
---- tests/reg-S4.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/reg-S4.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/reg-plot.Rout.save R-patched/tests/reg-plot.Rout.save
---- tests/reg-plot.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/reg-plot.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/reg-tests-2.R R-patched/tests/reg-tests-2.R
---- tests/reg-tests-2.R 2013-04-30 18:05:03.000000000 -0400
-+++ tests/reg-tests-2.R 2013-05-16 18:05:05.000000000 -0400
-@@ -2695,4 +2695,11 @@
-
- ## PR#15299 : adding a simple vector to a classed object produced a bad result:
- 1:2 + table(1:2)
--## Printed the class attribute in R <= 3.0.0
-\ No newline at end of file
-+## Printed the class attribute in R <= 3.0.0
-+
-+## PR#15311 : regmatches<- mishandled regexpr results.
-+ x <- c('1', 'B', '3')
-+ m <- regexpr('\\d', x)
-+ regmatches(x, m) <- c('A', 'C')
-+ print(x)
-+## Gave a warning and a wrong result up to 3.0.1
-\ No newline at end of file
-diff -ruN R-3.0.1/tests/reg-tests-2.Rout.save R-patched/tests/reg-tests-2.Rout.save
---- tests/reg-tests-2.Rout.save 2013-04-30 18:05:03.000000000 -0400
-+++ tests/reg-tests-2.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 Patched (2013-04-04 r62492) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-@@ -6397,15 +6397,15 @@
- > print.function
- function (x, ...)
- - attr(*, "srcref")=Class 'srcref' atomic [1:8] 1 19 1 63 19 63 1 1
-- .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x3c66fe8>
-+ .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x4c9d128>
- > f
- function ()
- - attr(*, "srcref")=Class 'srcref' atomic [1:8] 1 17 1 28 17 28 1 1
-- .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x3c46db0>
-+ .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x4c72208>
- - attr(*, "note")= chr "just a note"
- - attr(*, "yada")=function ()
- ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 2 24 2 48 24 48 2 2
-- .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x3c46db0>
-+ .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x4c72208>
- > rm(print.function)
- > ## auto-printing and printing differed up to R 2.9.x
- >
-@@ -7067,3 +7067,11 @@
- 2 3
- > ## Printed the class attribute in R <= 3.0.0
- >
-+> ## PR#15311 : regmatches<- mishandled regexpr results.
-+> x <- c('1', 'B', '3')
-+> m <- regexpr('\\d', x)
-+> regmatches(x, m) <- c('A', 'C')
-+> print(x)
-+[1] "A" "B" "C"
-+> ## Gave a warning and a wrong result up to 3.0.1
-+>
-diff -ruN R-3.0.1/tests/reg-tests-3.Rout.save R-patched/tests/reg-tests-3.Rout.save
---- tests/reg-tests-3.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/reg-tests-3.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
-diff -ruN R-3.0.1/tests/simple-true.Rout.save R-patched/tests/simple-true.Rout.save
---- tests/simple-true.Rout.save 2013-03-30 19:05:05.000000000 -0400
-+++ tests/simple-true.Rout.save 2013-05-24 18:05:05.000000000 -0400
-@@ -1,5 +1,5 @@
-
--R version 3.0.0 RC (2013-03-29 r62438) -- "Masked Marvel"
-+R version 3.0.1 Patched (2013-05-24 r62792) -- "Good Sport"
- Copyright (C) 2013 The R Foundation for Statistical Computing
- Platform: x86_64-unknown-linux-gnu (64-bit)
-
Modified: trunk/math/R/pkg-plist
===================================================================
--- trunk/math/R/pkg-plist 2015-05-09 03:12:24 UTC (rev 18826)
+++ trunk/math/R/pkg-plist 2015-05-09 03:16:06 UTC (rev 18827)
@@ -27,6 +27,9 @@
%%DOCSDIR%%/html/up.jpg
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
@@ -132,7 +135,6 @@
lib/R/library/MASS/CITATION
lib/R/library/MASS/DESCRIPTION
lib/R/library/MASS/INDEX
-lib/R/library/MASS/LICENCE
lib/R/library/MASS/Meta/Rd.rds
lib/R/library/MASS/Meta/data.rds
lib/R/library/MASS/Meta/hsearch.rds
@@ -223,6 +225,7 @@
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/symW.rda
lib/R/library/Matrix/external/test3comp.rda
lib/R/library/Matrix/external/utm300.rua
lib/R/library/Matrix/external/wrong.mtx
@@ -301,7 +304,6 @@
lib/R/library/class/CITATION
lib/R/library/class/DESCRIPTION
lib/R/library/class/INDEX
-lib/R/library/class/LICENCE
lib/R/library/class/Meta/Rd.rds
lib/R/library/class/Meta/hsearch.rds
lib/R/library/class/Meta/links.rds
@@ -611,23 +613,51 @@
lib/R/library/grid/Meta/links.rds
lib/R/library/grid/Meta/nsInfo.rds
lib/R/library/grid/Meta/package.rds
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/Meta/vignette.rds
lib/R/library/grid/NAMESPACE
lib/R/library/grid/R/grid
lib/R/library/grid/R/grid.rdb
lib/R/library/grid/R/grid.rdx
lib/R/library/grid/doc/changes.txt
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/displaylist.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/displaylist.Rnw
lib/R/library/grid/doc/displaylist.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/frame.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/frame.Rnw
lib/R/library/grid/doc/frame.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/grid.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/grid.Rnw
lib/R/library/grid/doc/grid.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/grobs.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/grobs.Rnw
lib/R/library/grid/doc/grobs.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/index.html
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/interactive.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/interactive.Rnw
lib/R/library/grid/doc/interactive.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/locndimn.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/locndimn.Rnw
lib/R/library/grid/doc/locndimn.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/moveline.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/moveline.Rnw
lib/R/library/grid/doc/moveline.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/nonfinite.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/nonfinite.Rnw
lib/R/library/grid/doc/nonfinite.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/plotexample.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/plotexample.Rnw
lib/R/library/grid/doc/plotexample.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/rotated.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/rotated.Rnw
lib/R/library/grid/doc/rotated.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/saveload.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/saveload.Rnw
lib/R/library/grid/doc/saveload.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/sharing.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/sharing.Rnw
lib/R/library/grid/doc/sharing.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/viewports.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/grid/doc/viewports.Rnw
lib/R/library/grid/doc/viewports.pdf
lib/R/library/grid/help/AnIndex
lib/R/library/grid/help/aliases.rds
@@ -670,6 +700,8 @@
%%NLS%%lib/R/library/lattice/po/de/LC_MESSAGES/R-lattice.mo
%%NLS%%lib/R/library/lattice/po/en at quot/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
@@ -715,7 +747,6 @@
lib/R/library/nlme/CITATION
lib/R/library/nlme/DESCRIPTION
lib/R/library/nlme/INDEX
-lib/R/library/nlme/LICENCE
lib/R/library/nlme/Meta/Rd.rds
lib/R/library/nlme/Meta/data.rds
lib/R/library/nlme/Meta/hsearch.rds
@@ -746,6 +777,8 @@
%%NLS%%lib/R/library/nlme/po/en at quot/LC_MESSAGES/nlme.mo
%%NLS%%lib/R/library/nlme/po/fr/LC_MESSAGES/R-nlme.mo
%%NLS%%lib/R/library/nlme/po/fr/LC_MESSAGES/nlme.mo
+%%NLS%%lib/R/library/nlme/po/ko/LC_MESSAGES/R-nlme.mo
+%%NLS%%lib/R/library/nlme/po/ko/LC_MESSAGES/nlme.mo
%%NLS%%lib/R/library/nlme/po/pl/LC_MESSAGES/R-nlme.mo
%%NLS%%lib/R/library/nlme/po/pl/LC_MESSAGES/nlme.mo
lib/R/library/nlme/scripts/ch01.R
@@ -759,7 +792,6 @@
lib/R/library/nnet/CITATION
lib/R/library/nnet/DESCRIPTION
lib/R/library/nnet/INDEX
-lib/R/library/nnet/LICENCE
lib/R/library/nnet/Meta/Rd.rds
lib/R/library/nnet/Meta/hsearch.rds
lib/R/library/nnet/Meta/links.rds
@@ -790,10 +822,14 @@
lib/R/library/parallel/Meta/links.rds
lib/R/library/parallel/Meta/nsInfo.rds
lib/R/library/parallel/Meta/package.rds
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/parallel/Meta/vignette.rds
lib/R/library/parallel/NAMESPACE
lib/R/library/parallel/R/parallel
lib/R/library/parallel/R/parallel.rdb
lib/R/library/parallel/R/parallel.rdx
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/parallel/doc/index.html
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/parallel/doc/parallel.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/parallel/doc/parallel.Rnw
lib/R/library/parallel/doc/parallel.pdf
lib/R/library/parallel/help/AnIndex
lib/R/library/parallel/help/aliases.rds
@@ -850,7 +886,6 @@
lib/R/library/spatial/CITATION
lib/R/library/spatial/DESCRIPTION
lib/R/library/spatial/INDEX
-lib/R/library/spatial/LICENCE
lib/R/library/spatial/Meta/Rd.rds
lib/R/library/spatial/Meta/hsearch.rds
lib/R/library/spatial/Meta/links.rds
@@ -1333,6 +1368,7 @@
lib/R/library/utils/Meta/links.rds
lib/R/library/utils/Meta/nsInfo.rds
lib/R/library/utils/Meta/package.rds
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/utils/Meta/vignette.rds
lib/R/library/utils/NAMESPACE
lib/R/library/utils/R/utils
lib/R/library/utils/R/utils.rdb
@@ -1339,7 +1375,10 @@
lib/R/library/utils/R/utils.rdx
lib/R/library/utils/Sweave/Sweave-test-1.Rnw
lib/R/library/utils/Sweave/example-1.Rnw
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/utils/doc/Sweave.R
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/utils/doc/Sweave.Rnw
lib/R/library/utils/doc/Sweave.pdf
+%%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/utils/doc/index.html
lib/R/library/utils/help/AnIndex
lib/R/library/utils/help/aliases.rds
lib/R/library/utils/help/paths.rds
@@ -1378,7 +1417,8 @@
lib/R/share/licenses/MIT
lib/R/share/licenses/license.db
lib/R/share/make/basepkg.mk
-lib/R/share/make/check.mk
+lib/R/share/make/check_vars_ini.mk
+lib/R/share/make/check_vars_out.mk
lib/R/share/make/clean.mk
lib/R/share/make/config.mk
lib/R/share/make/lazycomp.mk
@@ -1397,8 +1437,10 @@
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
%%LIBR%%libdata/pkgconfig/libR.pc
+man/man1/R.1.gz
+man/man1/Rscript.1.gz
+%%DOCSDIR%%/html/NEWS.2.html
%%DOCSDIR%%/manual/R-FAQ.html
%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-FAQ.pdf
%%DOCSDIR%%/manual/R-admin.html
@@ -1413,387 +1455,4 @@
%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-ints.pdf
%%DOCSDIR%%/manual/R-lang.html
%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-lang.pdf
-%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/refman.pdf
- at dirrm lib/R/share/texmf/tex/latex
- at dirrm lib/R/share/texmf/tex
- at dirrm lib/R/share/texmf/bibtex/bst
- at dirrm lib/R/share/texmf/bibtex/bib
- at dirrm lib/R/share/texmf/bibtex
- at dirrm lib/R/share/texmf
- at dirrm lib/R/share/sh
- at dirrm lib/R/share/make
- at dirrm lib/R/share/licenses
- at dirrm lib/R/share/java
- at dirrm lib/R/share/encodings
- at dirrm lib/R/share/dictionaries
- at dirrm lib/R/share/R
- at dirrm lib/R/share
- at dirrm lib/R/modules
- at dirrm lib/R/library/utils/misc
- at dirrm lib/R/library/utils/libs
- at dirrm lib/R/library/utils/html
- at dirrm lib/R/library/utils/help
- at dirrm lib/R/library/utils/doc
- at dirrm lib/R/library/utils/Sweave
- at dirrm lib/R/library/utils/R
- at dirrm lib/R/library/utils/Meta
- at dirrm lib/R/library/utils
-%%NLS%%@dirrm lib/R/library/translations/zh_TW/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/zh_TW
-%%NLS%%@dirrm lib/R/library/translations/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/zh_CN
-%%NLS%%@dirrm lib/R/library/translations/tr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/tr
-%%NLS%%@dirrm lib/R/library/translations/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/ru
-%%NLS%%@dirrm lib/R/library/translations/pt_BR/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/pt_BR
-%%NLS%%@dirrm lib/R/library/translations/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/pl
-%%NLS%%@dirrm lib/R/library/translations/nn/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/nn
-%%NLS%%@dirrm lib/R/library/translations/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/ko
-%%NLS%%@dirrm lib/R/library/translations/ja/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/ja
-%%NLS%%@dirrm lib/R/library/translations/it/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/it
-%%NLS%%@dirrm lib/R/library/translations/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/fr
-%%NLS%%@dirrm lib/R/library/translations/fa/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/fa
-%%NLS%%@dirrm lib/R/library/translations/es/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/es
-%%NLS%%@dirrm lib/R/library/translations/en_GB/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/en_GB
-%%NLS%%@dirrm lib/R/library/translations/en at quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/en at quot
-%%NLS%%@dirrm lib/R/library/translations/en/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/en
-%%NLS%%@dirrm lib/R/library/translations/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/de
-%%NLS%%@dirrm lib/R/library/translations/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/translations/da
- at dirrm lib/R/library/translations
- at dirrm lib/R/library/tools/libs
- at dirrm lib/R/library/tools/html
- at dirrm lib/R/library/tools/help
- at dirrm lib/R/library/tools/R
- at dirrm lib/R/library/tools/Meta
- at dirrm lib/R/library/tools
-%%TCLTK%%@dirrm lib/R/library/tcltk/libs
- at dirrm lib/R/library/tcltk/html
- at dirrm lib/R/library/tcltk/help
- at dirrm lib/R/library/tcltk/exec
- at dirrm lib/R/library/tcltk/demo
- at dirrm lib/R/library/tcltk/R
- at dirrm lib/R/library/tcltk/Meta
- at dirrm lib/R/library/tcltk
- at dirrm lib/R/library/survival/libs
- at dirrm lib/R/library/survival/html
- at dirrm lib/R/library/survival/help
- at dirrm lib/R/library/survival/doc
- at dirrm lib/R/library/survival/data
- at dirrm lib/R/library/survival/R
- at dirrm lib/R/library/survival/Meta
- at dirrm lib/R/library/survival
- at dirrm lib/R/library/stats/libs
- at dirrm lib/R/library/stats/html
- at dirrm lib/R/library/stats/help
- at dirrm lib/R/library/stats/demo
- at dirrm lib/R/library/stats/R
- at dirrm lib/R/library/stats/Meta
- at dirrm lib/R/library/stats4/html
- at dirrm lib/R/library/stats4/help
- at dirrm lib/R/library/stats4/R
- at dirrm lib/R/library/stats4/Meta
- at dirrm lib/R/library/stats4
- at dirrm lib/R/library/stats
- at dirrm lib/R/library/splines/libs
- at dirrm lib/R/library/splines/html
- at dirrm lib/R/library/splines/help
- at dirrm lib/R/library/splines/R
- at dirrm lib/R/library/splines/Meta
- at dirrm lib/R/library/splines
- at dirrm lib/R/library/spatial/ppdata
-%%NLS%%@dirrm lib/R/library/spatial/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/spatial/po/pl
-%%NLS%%@dirrm lib/R/library/spatial/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/spatial/po/fr
-%%NLS%%@dirrm lib/R/library/spatial/po/en at quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/spatial/po/en at quot
-%%NLS%%@dirrm lib/R/library/spatial/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/spatial/po/de
-%%NLS%%@dirrm lib/R/library/spatial/po
- at dirrm lib/R/library/spatial/libs
- at dirrm lib/R/library/spatial/html
- at dirrm lib/R/library/spatial/help
- at dirrm lib/R/library/spatial/R
- at dirrm lib/R/library/spatial/Meta
- at dirrm lib/R/library/spatial
-%%NLS%%@dirrm lib/R/library/rpart/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/rpart/po/ru
-%%NLS%%@dirrm lib/R/library/rpart/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/rpart/po/pl
-%%NLS%%@dirrm lib/R/library/rpart/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/rpart/po/ko
-%%NLS%%@dirrm lib/R/library/rpart/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/rpart/po/fr
-%%NLS%%@dirrm lib/R/library/rpart/po/en at quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/rpart/po/en at quot
-%%NLS%%@dirrm lib/R/library/rpart/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/rpart/po/de
-%%NLS%%@dirrm lib/R/library/rpart/po
- at dirrm lib/R/library/rpart/libs
- at dirrm lib/R/library/rpart/html
- at dirrm lib/R/library/rpart/help
- at dirrm lib/R/library/rpart/doc
- at dirrm lib/R/library/rpart/data
- at dirrm lib/R/library/rpart/R
- at dirrm lib/R/library/rpart/Meta
- at dirrm lib/R/library/rpart
- at dirrm lib/R/library/parallel/libs
- at dirrm lib/R/library/parallel/html
- at dirrm lib/R/library/parallel/help
- at dirrm lib/R/library/parallel/doc
- at dirrm lib/R/library/parallel/R
- at dirrm lib/R/library/parallel/Meta
- at dirrm lib/R/library/parallel
-%%NLS%%@dirrm lib/R/library/nnet/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/nnet/po/pl
-%%NLS%%@dirrm lib/R/library/nnet/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/nnet/po/ko
-%%NLS%%@dirrm lib/R/library/nnet/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/nnet/po/fr
-%%NLS%%@dirrm lib/R/library/nnet/po/en at quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/nnet/po/en at quot
-%%NLS%%@dirrm lib/R/library/nnet/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/nnet/po/de
-%%NLS%%@dirrm lib/R/library/nnet/po
- at dirrm lib/R/library/nnet/libs
- at dirrm lib/R/library/nnet/html
- at dirrm lib/R/library/nnet/help
- at dirrm lib/R/library/nnet/R
- at dirrm lib/R/library/nnet/Meta
- at dirrm lib/R/library/nnet
- at dirrm lib/R/library/nlme/scripts
-%%NLS%%@dirrm lib/R/library/nlme/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/nlme/po/pl
-%%NLS%%@dirrm lib/R/library/nlme/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/nlme/po/fr
-%%NLS%%@dirrm lib/R/library/nlme/po/en at quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/nlme/po/en at quot
-%%NLS%%@dirrm lib/R/library/nlme/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/nlme/po/de
-%%NLS%%@dirrm lib/R/library/nlme/po
- at dirrm lib/R/library/nlme/mlbook
- at dirrm lib/R/library/nlme/libs
- at dirrm lib/R/library/nlme/html
- at dirrm lib/R/library/nlme/help
- at dirrm lib/R/library/nlme/data
- at dirrm lib/R/library/nlme/R
- at dirrm lib/R/library/nlme/Meta
- at dirrm lib/R/library/nlme
- at dirrm lib/R/library/mgcv/libs
- at dirrm lib/R/library/mgcv/html
- at dirrm lib/R/library/mgcv/help
- at dirrm lib/R/library/mgcv/data
- at dirrm lib/R/library/mgcv/R
- at dirrm lib/R/library/mgcv/Meta
- at dirrm lib/R/library/mgcv
- at dirrm lib/R/library/methods/libs
- at dirrm lib/R/library/methods/html
- at dirrm lib/R/library/methods/help
- at dirrm lib/R/library/methods/R
- at dirrm lib/R/library/methods/Meta
- at dirrm lib/R/library/methods
-%%NLS%%@dirrm lib/R/library/lattice/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/lattice/po/fr
-%%NLS%%@dirrm lib/R/library/lattice/po/en at quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/lattice/po/en at quot
-%%NLS%%@dirrm lib/R/library/lattice/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/lattice/po/de
-%%NLS%%@dirrm lib/R/library/lattice/po
- at dirrm lib/R/library/lattice/libs
- at dirrm lib/R/library/lattice/html
- at dirrm lib/R/library/lattice/help
- at dirrm lib/R/library/lattice/demo
- at dirrm lib/R/library/lattice/data
- at dirrm lib/R/library/lattice/R
- at dirrm lib/R/library/lattice/Meta
- at dirrm lib/R/library/lattice
- at dirrm lib/R/library/grid/libs
- at dirrm lib/R/library/grid/html
- at dirrm lib/R/library/grid/help
- at dirrm lib/R/library/grid/doc
- at dirrm lib/R/library/grid/R
- at dirrm lib/R/library/grid/Meta
- at dirrm lib/R/library/grid
- at dirrm lib/R/library/graphics/libs
- at dirrm lib/R/library/graphics/html
- at dirrm lib/R/library/graphics/help/figures
- at dirrm lib/R/library/graphics/help
- at dirrm lib/R/library/graphics/demo
- at dirrm lib/R/library/graphics/R
- at dirrm lib/R/library/graphics/Meta
- at dirrm lib/R/library/graphics
- at dirrm lib/R/library/grDevices/libs
- at dirrm lib/R/library/grDevices/icc
- at dirrm lib/R/library/grDevices/html
- at dirrm lib/R/library/grDevices/help
- at dirrm lib/R/library/grDevices/enc
- at dirrm lib/R/library/grDevices/demo
- at dirrm lib/R/library/grDevices/afm
- at dirrm lib/R/library/grDevices/R
- at dirrm lib/R/library/grDevices/Meta
- at dirrm lib/R/library/grDevices
-%%NLS%%@dirrm lib/R/library/foreign/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/foreign/po/pl
-%%NLS%%@dirrm lib/R/library/foreign/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/foreign/po/fr
-%%NLS%%@dirrm lib/R/library/foreign/po/en at quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/foreign/po/en at quot
-%%NLS%%@dirrm lib/R/library/foreign/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/foreign/po/de
-%%NLS%%@dirrm lib/R/library/foreign/po
- at dirrm lib/R/library/foreign/libs
- at dirrm lib/R/library/foreign/html
- at dirrm lib/R/library/foreign/help
- at dirrm lib/R/library/foreign/files
- at dirrm lib/R/library/foreign/R
- at dirrm lib/R/library/foreign/Meta
- at dirrm lib/R/library/foreign
- at dirrm lib/R/library/datasets/html
- at dirrm lib/R/library/datasets/help
- at dirrm lib/R/library/datasets/data
- at dirrm lib/R/library/datasets/Meta
- at dirrm lib/R/library/datasets
- at dirrm lib/R/library/compiler/html
- at dirrm lib/R/library/compiler/help
- at dirrm lib/R/library/compiler/R
- at dirrm lib/R/library/compiler/Meta
- at dirrm lib/R/library/compiler
- at dirrm lib/R/library/codetools/html
- at dirrm lib/R/library/codetools/help
- at dirrm lib/R/library/codetools/R
- at dirrm lib/R/library/codetools/Meta
- at dirrm lib/R/library/codetools
-%%NLS%%@dirrm lib/R/library/cluster/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/cluster/po/pl
-%%NLS%%@dirrm lib/R/library/cluster/po/en at quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/cluster/po/en at quot
-%%NLS%%@dirrm lib/R/library/cluster/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/cluster/po/de
-%%NLS%%@dirrm lib/R/library/cluster/po
- at dirrm lib/R/library/cluster/libs
- at dirrm lib/R/library/cluster/html
- at dirrm lib/R/library/cluster/help
- at dirrm lib/R/library/cluster/data
- at dirrm lib/R/library/cluster/R
- at dirrm lib/R/library/cluster/Meta
- at dirrm lib/R/library/cluster
-%%NLS%%@dirrm lib/R/library/class/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/class/po/pl
-%%NLS%%@dirrm lib/R/library/class/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/class/po/ko
-%%NLS%%@dirrm lib/R/library/class/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/class/po/fr
-%%NLS%%@dirrm lib/R/library/class/po/en at quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/class/po/en at quot
-%%NLS%%@dirrm lib/R/library/class/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/class/po/de
-%%NLS%%@dirrm lib/R/library/class/po
- at dirrm lib/R/library/class/libs
- at dirrm lib/R/library/class/html
- at dirrm lib/R/library/class/help
- at dirrm lib/R/library/class/R
- at dirrm lib/R/library/class/Meta
- at dirrm lib/R/library/class
-%%NLS%%@dirrm lib/R/library/boot/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/boot/po/ru
-%%NLS%%@dirrm lib/R/library/boot/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/boot/po/pl
-%%NLS%%@dirrm lib/R/library/boot/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/boot/po/ko
-%%NLS%%@dirrm lib/R/library/boot/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/boot/po/fr
-%%NLS%%@dirrm lib/R/library/boot/po/en at quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/boot/po/en at quot
-%%NLS%%@dirrm lib/R/library/boot/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/boot/po/de
-%%NLS%%@dirrm lib/R/library/boot/po
- at dirrm lib/R/library/boot/html
- at dirrm lib/R/library/boot/help
- at dirrm lib/R/library/boot/data
- at dirrm lib/R/library/boot/R
- at dirrm lib/R/library/boot/Meta
- at dirrm lib/R/library/boot
- at dirrm lib/R/library/base/html
- at dirrm lib/R/library/base/help
- at dirrm lib/R/library/base/demo
- at dirrm lib/R/library/base/R
- at dirrm lib/R/library/base/Meta
- at dirrm lib/R/library/base
-%%NLS%%@dirrm lib/R/library/Matrix/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/Matrix/po/pl
-%%NLS%%@dirrm lib/R/library/Matrix/po/en at quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/Matrix/po/en at quot
-%%NLS%%@dirrm lib/R/library/Matrix/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/Matrix/po/de
-%%NLS%%@dirrm lib/R/library/Matrix/po
- at dirrm lib/R/library/Matrix/libs
- at dirrm lib/R/library/Matrix/include
- at dirrm lib/R/library/Matrix/html
- at dirrm lib/R/library/Matrix/help
- at dirrm lib/R/library/Matrix/external
- at dirrm lib/R/library/Matrix/doc/SuiteSparse
- at dirrm lib/R/library/Matrix/doc
- at dirrm lib/R/library/Matrix/data
- at dirrm lib/R/library/Matrix/R
- at dirrm lib/R/library/Matrix/Meta
- at dirrm lib/R/library/Matrix
- at dirrm lib/R/library/MASS/scripts
-%%NLS%%@dirrm lib/R/library/MASS/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/MASS/po/pl
-%%NLS%%@dirrm lib/R/library/MASS/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/MASS/po/ko
-%%NLS%%@dirrm lib/R/library/MASS/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/MASS/po/fr
-%%NLS%%@dirrm lib/R/library/MASS/po/en at quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/MASS/po/en at quot
-%%NLS%%@dirrm lib/R/library/MASS/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/MASS/po/de
-%%NLS%%@dirrm lib/R/library/MASS/po
- at dirrm lib/R/library/MASS/libs
- at dirrm lib/R/library/MASS/html
- at dirrm lib/R/library/MASS/help
- at dirrm lib/R/library/MASS/data
- at dirrm lib/R/library/MASS/R
- at dirrm lib/R/library/MASS/Meta
- at dirrm lib/R/library/MASS
-%%NLS%%@dirrm lib/R/library/KernSmooth/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/KernSmooth/po/pl
-%%NLS%%@dirrm lib/R/library/KernSmooth/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/KernSmooth/po/ko
-%%NLS%%@dirrm lib/R/library/KernSmooth/po/en at quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/KernSmooth/po/en at quot
-%%NLS%%@dirrm lib/R/library/KernSmooth/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/KernSmooth/po/de
-%%NLS%%@dirrm lib/R/library/KernSmooth/po
- at dirrm lib/R/library/KernSmooth/libs
- at dirrm lib/R/library/KernSmooth/html
- at dirrm lib/R/library/KernSmooth/help
- at dirrm lib/R/library/KernSmooth/R
- at dirrm lib/R/library/KernSmooth/Meta
- at dirrm lib/R/library/KernSmooth
- at dirrmtry lib/R/library
- at dirrmtry lib/R/lib
- at dirrm lib/R/include/R_ext
- at dirrm lib/R/include
- at dirrm lib/R/etc
- at dirrm lib/R/bin/exec
- at dirrm lib/R/bin
- at dirrmtry lib/R
- at dirrm %%DOCSDIR%%/manual
- at dirrm %%DOCSDIR%%/html
- at dirrm %%DOCSDIR%%
+%%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/fullrefman.pdf
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