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authorbf <bf@FreeBSD.org>2013-05-28 23:15:05 +0800
committerbf <bf@FreeBSD.org>2013-05-28 23:15:05 +0800
commit7c5db22c2746a52cfe09a5cb41aea8647b3fcd94 (patch)
tree415589d9c68c0b0770aa00cfd4495ce30df83a29 /math/R
parentce20681bb0d550df419bfd27b8b856c7f07f1975 (diff)
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Update math/R to 3.0.1-patched, and adjust dependent ports;
synchronize math/rpy with upstream repository Reviewed by: wen Approved by: wen, tota
Diffstat (limited to 'math/R')
-rw-r--r--math/R/Makefile65
-rw-r--r--math/R/distinfo4
-rw-r--r--math/R/files/patch-201305262831
-rw-r--r--math/R/files/patch-doc__manual__refman.top33
-rw-r--r--math/R/pkg-plist934
5 files changed, 3223 insertions, 644 deletions
diff --git a/math/R/Makefile b/math/R/Makefile
index b64dea7c1dbb..82cfb4618c59 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -2,22 +2,23 @@
# $FreeBSD$
PORTNAME?= R
-PORTVERSION= 2.15.3
+PORTVERSION= 3.0.1
CATEGORIES= math lang
-MASTER_SITES= http://cran.r-project.org/src/base/R-2/ \
- ftp://cran.r-project.org/pub/R/src/base/R-2/ \
- http://cran.at.r-project.org/src/base/R-2/ \
- http://cran.au.r-project.org/src/base/R-2/ \
- http://cran.br.r-project.org/src/base/R-2/ \
- http://cran.ch.r-project.org/src/base/R-2/ \
- http://cran.es.r-project.org/src/base/R-2/ \
- http://cran.dk.r-project.org/src/base/R-2/ \
- http://cran.uk.r-project.org/src/base/R-2/ \
- http://cran.us.r-project.org/src/base/R-2/ \
- ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/src/base/R-2/ \
- http://lib.stat.cmu.edu/R/CRAN/src/base/R-2/ \
- http://cran.stat.ucla.edu/src/base/R-2/ \
- http://probability.ca/cran/src/base/R-2/
+MASTER_SITES= http://cran.r-project.org/%SUBDIR%/ \
+ ftp://cran.r-project.org/pub/R/%SUBDIR%/ \
+ http://cran.at.r-project.org/%SUBDIR%/ \
+ http://cran.au.r-project.org/%SUBDIR%/ \
+ http://cran.br.r-project.org/%SUBDIR%/ \
+ http://cran.ch.r-project.org/%SUBDIR%/ \
+ http://cran.es.r-project.org/%SUBDIR%/ \
+ http://cran.dk.r-project.org/%SUBDIR%/ \
+ http://cran.uk.r-project.org/%SUBDIR%/ \
+ http://cran.us.r-project.org/%SUBDIR%/ \
+ ftp://ftp.u-aizu.ac.jp/pub/lang/R/CRAN/%SUBDIR%/ \
+ http://lib.stat.cmu.edu/R/CRAN/%SUBDIR%/ \
+ http://cran.stat.ucla.edu/%SUBDIR%/ \
+ http://probability.ca/cran/%SUBDIR%/
+MASTER_SITE_SUBDIR= src/base/R-${PORTVERSION:C|\..*||}
DISTNAME= R-${PORTVERSION}
MAINTAINER= bf@FreeBSD.org
@@ -27,7 +28,8 @@ LICENSE= GPLv2
BUILD_DEPENDS= ${LOCALBASE}/bin/gsed:${PORTSDIR}/textproc/gsed
-CONFIGURE_ENV= SED="${LOCALBASE}/bin/gsed"
+CONFIGURE_ENV= SED="${LOCALBASE}/bin/gsed" \
+ ac_cv_have_decl_powl=yes ac_cv_have_decl_log1pl=yes
OPTIONS_DEFINE= MISSING
@@ -59,10 +61,12 @@ 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
-OPTIONS_DEFAULT= ICU PCRE_PORT THREADS
+OPTIONS_DEFAULT+= ICU PCRE_PORT THREADS
.if !defined(LIBR_SLAVEPORT)
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
MAN1= R.1 Rscript.1
@@ -92,12 +96,11 @@ USES+= iconv
.endif # LIBRMATH_SLAVEPORT
GNU_CONFIGURE= yes
MAKE_JOBS_UNSAFE= yes
-R_SOVERSION= 0
+R_SOVERSION= 1
RBLAS_SOVERSION= 2
RLAPACK_SOVERSION= 4
RMATH_SOVERSION= 0
USE_FORTRAN= yes
-USE_PERL5_BUILD= yes
.include <bsd.port.options.mk>
@@ -146,7 +149,7 @@ CONFIGURE_ARGS+= --without-ICU
.endif
.if ${PORT_OPTIONS:MNLS}
-USES+= gettext
+USES+= gettext
PLIST_SUB+= NLS=""
.else
CONFIGURE_ARGS+= --disable-nls
@@ -242,9 +245,9 @@ INFO= R-FAQ R-admin R-data R-exts R-intro R-lang
.endif
.if ${PORT_OPTIONS:MPDF_MANUALS} && ${PORT_OPTIONS:MDOCS}
-BROKEN = The PDF_MANUALS option cannot be used, because\
- print/texinfo is incompatible with print/teTeX-base
-USE_TEX= tex:build
+BROKEN= The PDF_MANUALS option cannot be used, because it\
+ requires broken components of texlive
+USE_TEX= texlive pdftex:build
BUILD_DEPENDS += texi2dvi:${PORTSDIR}/print/texinfo
ALL_TARGET+= pdf
CONFIGURE_ENV += INSTALL_INFO="${LOCALBASE}/bin/install-info" \
@@ -259,9 +262,15 @@ PLIST_SUB+= PDF_MANUAL="@comment "
post-patch:
.if !${PORT_OPTIONS:MMISSING}
- @${REINPLACE_CMD} -e 's|logl(|(long double)logq((__float128)|' \
+.if ${OSVERSION} < 1000016
+ @${REINPLACE_CMD} -e 's/# define EXP expl/# define EXP(x) (long double)expq((__float128)(x))/' \
+ ${WRKSRC}/src/nmath/pnchisq.c
+.endif
+ @${REINPLACE_CMD} -Ee 's/(log)(1p)?l\(/(long double)\1\2q((__float128)/' \
${WRKSRC}/src/nmath/dnbeta.c \
${WRKSRC}/src/nmath/pnbeta.c
+ @${REINPLACE_CMD} -Ee 's/powl\((.*)(long double)/(long double)powq((__float128)\1__float128/' \
+ ${WRKSRC}/src/main/format.c
.endif
@${REINPLACE_CMD} -e \
'\|#include <math.h>|{x;s|^.*$$|#include ${LIBMH}|;H;x;}' \
@@ -277,8 +286,7 @@ post-patch:
${WRKSRC}/src/scripts/javareconf
@${REINPLACE_CMD} -e "s|/usr/local|${LOCALBASE}|g" \
${WRKSRC}/configure \
- ${WRKSRC}/config.site \
- ${WRKSRC}/src/extra/tzone/tzfile.h \
+ ${WRKSRC}/src/library/profile/Rprofile.unix \
${WRKSRC}/src/scripts/javareconf
.if !defined(LIBRMATH_SLAVEPORT)
.if !${PORT_OPTIONS:MNLS}
@@ -287,6 +295,8 @@ post-patch:
${TAR} -czf temptgz --exclude='*/po/*' @$$tarfile ; \
${MV} temptgz $$tarfile ; \
done)
+ @${REINPLACE_CMD} -e '/ls -d $$(srcdir)\/inst/d' \
+ ${WRKSRC}/src/library/translations/Makefile.in
.endif
.if !${PORT_OPTIONS:MMISSING}
@@ -312,6 +322,9 @@ do-install:
.else # LIBR_SLAVEPORT
+pre-configure-script:
+ @${FIND} ${WRKSRC} \( -name '*.orig' -o -name '*.bak' \) -delete
+
check regression-test test: build
@(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} LANGUAGE=en \
LC_COLLATE=C LC_TIME=C ${MAKE} ${_MAKE_JOBS} ${MAKE_ARGS} \
diff --git a/math/R/distinfo b/math/R/distinfo
index 8a5ff735289e..32a127b92334 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,2 +1,2 @@
-SHA256 (R-2.15.3.tar.gz) = c583a38f8dad3bc012c08116f4ba1eb2182cadfad4b0f8d7bd3cdba24bc255d6
-SIZE (R-2.15.3.tar.gz) = 25409925
+SHA256 (R-3.0.1.tar.gz) = af90488af3141103b211dc81b6f17d1f0faf4f17684c579a32dfeb25d0d87134
+SIZE (R-3.0.1.tar.gz) = 25508280
diff --git a/math/R/files/patch-20130526 b/math/R/files/patch-20130526
new file mode 100644
index 000000000000..5f3c74252ae9
--- /dev/null
+++ b/math/R/files/patch-20130526
@@ -0,0 +1,2831 @@
+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>&lsquo;<span class="file">Rdefines.h</span>&rsquo; has been tweaked so it can be included in
++C++ code with &lsquo;<span class="file">R_exts/Boolean.h</span>&rsquo; (which is included by
++&lsquo;<span class="file">R.h</span>&rsquo;). Note though that &lsquo;<span class="file">Rdefines.h</span>&rsquo; is not kept
++up-to-date, and &lsquo;<span class="file">Rinternals.h</span>&rsquo; 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&lt;-()</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 &lsquo;<span class="file">etc/Rconsole</span>&rsquo; and
++&lsquo;<span class="file">etc/Rprofile.site</span>&rsquo; 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 &ndash; 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 &lsquo;<samp><span class="samp">ALLUSERS</span></samp>&rsquo;, &lsquo;<samp><span class="samp">INSTALLDIR</span></samp>&rsquo; (something like
+-<samp><span class="file">c:\Program Files\R\R-3.0.1</span></samp>) and &lsquo;<samp><span class="samp">RMENU</span></samp>&rsquo; (the path
++<samp><span class="file">c:\Program Files\R\R-3.0.1patched</span></samp>) and &lsquo;<samp><span class="samp">RMENU</span></samp>&rsquo; (the path
+ to the &lsquo;<samp><span class="samp">R</span></samp>&rsquo; folder on the start menu) and &lsquo;<samp><span class="samp">STARTDIR</span></samp>&rsquo; (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
+
+-@macro eqn {t, a}
+ @iftex
++@macro eqn {t, a}
+ @tex
+ $\t\$%
+ @end tex
++@end macro
+ @end iftex
+ @ifnottex
+-\a\@c
+-@end ifnottex
++@macro eqn {t, a}
++\a\
+ @end macro
++@end ifnottex
+
+ @macro pkg {p}
+ @strong{\p\}
+diff -ruN R-3.0.1/doc/manual/R-exts.R R-patched/doc/manual/R-exts.R
+--- doc/manual/R-exts.R 2011-06-17 06:39:34.000000000 -0400
++++ doc/manual/R-exts.R 2013-05-26 18:05:04.000000000 -0400
+@@ -33,9 +33,6 @@
+ u <- rep(1, 5)
+ conv(u, u)
+
+-conv <- function(a, b) .Call("convolve2b", a, b)
+-conv(u, u)
+-
+ convE <- function(a, b) .External("convolveE", a, b)
+ convE(u, u)
+
+@@ -71,7 +68,7 @@
+
+ ## ----- numerical derivatives -----
+
+-numeric.deriv <- function(expr, theta, rho=sys.frame(sys.parent()))
++numeric.deriv <- function(expr, theta, rho = sys.frame(sys.parent()))
+ {
+ eps <- sqrt(.Machine$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
+
++@cindex CRAN
++@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
++@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.
+
+-@node Writing package vignettes, Submitting a package to CRAN, Checking and building packages, Creating R packages
++@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.
+
+-@node Submitting a package to CRAN, Package namespaces, Writing package vignettes, Creating R packages
+-@section Submitting a package to @acronym{CRAN}
+-@cindex CRAN
+-@cindex CRAN submission
+-@cindex Submitting to CRAN
+-
+-@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
+-@uref{http://CRAN.R-project.org/banner.shtml#submitting}.
+-
+-@node Package namespaces, Writing portable packages, Submitting a package to CRAN, Creating R packages
++@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$$r_arch,
+- package="packB", mustWork=TRUE))' \
++PKGB_PATH=`echo 'library(packB);
++ cat(system.file("libs", package="packB", mustWork=TRUE))' \
+ | "$@{R_HOME@}/bin/R" --vanilla --slave`
+-PKG_LIBS="$(PKGB_PATH)/libpackB.a"
++PKG_LIBS="$(PKGB_PATH)$(R_ARCH)/libpackB.a"
+ @end example
+
+-@noindent
+-which will give an empty path component if sub-architectures are not in
+-use (but that works on current platforms).
+-
+ For a dynamic library @file{packB/libs/libpackB.so}
+ (@file{packB/libs/libpackB.dylib} on OS X: note that you cannot link to
+ a shared object, @file{.so} on that platform) we could use
+
+ @example
+-PKGB_PATH=`echo 'cat(system.file("libs", .Platform$$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
+-@ref{Interface functions .Call and .External} for details on
+-@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
++@file{Rinternals.h} or some @Sl{}-compatibility macros@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
++@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@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
+-@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@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 @file{@var{R_INCLUDE_DIR}} (default
++@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
+
+-@noindent
+-and then those in @file{Rdefines.h}:
+-
+-@example
+-@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);
+-@end group
+-@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@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_@var{XXX}} macros defined in
+-@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
++@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
+-@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}.
++@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,
+-
+-@example
+-PROTECT(@var{newSexp} = coerceVector(@var{oldSexp}, REALSXP));
+-@end example
+-
+-@noindent
+-or
++object, you can change the type by using
+
+ @example
+-PROTECT(@var{newSexp} = AS_NUMERIC(@var{oldSexp}));
++@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;
+-@end group
+-
+-@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];
+ @}
+-@end group
+
+-@group
+- PROTECT(dim = allocVector(INTSXP, 2));
+- INTEGER(dim)[0] = nx; INTEGER(dim)[1] = ny;
+- setAttrib(ans, R_DimSymbol, dim);
+-@end group
+-
+-@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:
++
++@example
++@group
++ SEXP version = PROTECT(ScalarReal(3.0));
++ setAttrib(ans, install("version"), version);
++ UNPROTECT(1);
++@end group
++@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
+-
+-@example
+-@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);
+-@}
+-@end group
+-@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
+
+-@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@footnote{ACM Software Systems award, 1998:
++@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.
+-@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.
++@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
+
++@iftex
+ @macro xTx{}
+- @eqn{@strong{x}^T @strong{x}, x'x}
++@tex
++$@strong{x}^T @strong{x}$%
++@end tex
+ @end macro
+ @macro xxT{}
+- @eqn{@strong{x}@strong{x}^T, x x'}
++@tex
++$@strong{x}@strong{x}^T$%
++@end tex
+ @end macro
++@end iftex
++
++@ifnottex
++@macro xTx{}
++x'x
++@end macro
++@macro xxT{}
++x x'
++@end macro
++@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
+-@xTx{} or @xxT{} is @code{crossprod(x)} or @code{x %o% x}
+-respectively.}
++@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@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@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@footnote{Under UNIX, the utilities
++@command{sed} or@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,
+-@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
++@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
++@code{X11()} under UNIX, @code{windows()} under Windows and
++@code{quartz()} under OS X. A new device can always be opened by
++@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: 62610 $'
++revision='$Revision: 62759 $'
+ 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)
+
diff --git a/math/R/files/patch-doc__manual__refman.top b/math/R/files/patch-doc__manual__refman.top
deleted file mode 100644
index 9d239cbd25f1..000000000000
--- a/math/R/files/patch-doc__manual__refman.top
+++ /dev/null
@@ -1,33 +0,0 @@
---- doc/manual/refman.top.orig 2011-11-23 12:21:46.000000000 -0500
-+++ doc/manual/refman.top 2011-11-23 12:22:31.000000000 -0500
-@@ -4,18 +4,18 @@
-
- %% Set PDF 1.5 and compression, including object compression
- %% Needed for MiKTeX -- most other distributions default to this
--\ifx\pdfoutput\undefined
--\else
-- \ifx\pdfoutput\relax
-- \else
-- \ifnum\pdfoutput>0
-- % PDF output
-- \pdfminorversion=5
-- \pdfcompresslevel=9
-- \pdfobjcompresslevel=2
-- \fi
-- \fi
--\fi
-+%%\ifx\pdfoutput\undefined
-+%%\else
-+%% \ifx\pdfoutput\relax
-+%% \else
-+%% \ifnum\pdfoutput>0
-+%% % PDF output
-+%% \pdfminorversion=5
-+%% \pdfcompresslevel=9
-+%% \pdfobjcompresslevel=2
-+%% \fi
-+%% \fi
-+%%\fi
-
- \makeatletter
- \renewcommand\@pnumwidth{2.05em} % over 1000 pages
diff --git a/math/R/pkg-plist b/math/R/pkg-plist
index dd58f67ee34a..b64d35b49c92 100644
--- a/math/R/pkg-plist
+++ b/math/R/pkg-plist
@@ -56,6 +56,7 @@ lib/R/bin/pager
lib/R/bin/rtags
lib/R/etc/Makeconf
lib/R/etc/Renviron
+lib/R/etc/javaconf
lib/R/etc/ldpaths
lib/R/etc/repositories
lib/R/include/Rconfig.h
@@ -67,6 +68,7 @@ lib/R/include/R_ext/BLAS.h
lib/R/include/R_ext/Boolean.h
lib/R/include/R_ext/Callbacks.h
lib/R/include/R_ext/Complex.h
+lib/R/include/R_ext/Connections.h
lib/R/include/R_ext/Constants.h
lib/R/include/R_ext/Error.h
lib/R/include/R_ext/GetX11Image.h
@@ -80,7 +82,6 @@ lib/R/include/R_ext/Parse.h
lib/R/include/R_ext/Print.h
lib/R/include/R_ext/PrtUtil.h
lib/R/include/R_ext/QuartzDevice.h
-lib/R/include/R_ext/RConverters.h
lib/R/include/R_ext/RS.h
lib/R/include/R_ext/RStartup.h
lib/R/include/R_ext/Random.h
@@ -91,7 +92,6 @@ lib/R/include/R_ext/Utils.h
lib/R/include/R_ext/Visibility.h
lib/R/include/R_ext/eventloop.h
lib/R/include/R_ext/libextern.h
-lib/R/include/R_ext/rlocale.h
lib/R/include/R_ext/stats_package.h
lib/R/include/R_ext/stats_stubs.h
lib/R/include/R.h
@@ -108,7 +108,6 @@ lib/R/include/S.h
%%LIBR%%lib/R/lib/libR.so.%%R_SOVERSION%%
lib/R/library/KernSmooth/DESCRIPTION
lib/R/library/KernSmooth/INDEX
-lib/R/library/KernSmooth/LICENCE
lib/R/library/KernSmooth/Meta/Rd.rds
lib/R/library/KernSmooth/Meta/hsearch.rds
lib/R/library/KernSmooth/Meta/links.rds
@@ -128,6 +127,7 @@ lib/R/library/KernSmooth/html/R.css
lib/R/library/KernSmooth/libs/KernSmooth.so
%%NLS%%lib/R/library/KernSmooth/po/de/LC_MESSAGES/R-KernSmooth.mo
%%NLS%%lib/R/library/KernSmooth/po/en@quot/LC_MESSAGES/R-KernSmooth.mo
+%%NLS%%lib/R/library/KernSmooth/po/ko/LC_MESSAGES/R-KernSmooth.mo
%%NLS%%lib/R/library/KernSmooth/po/pl/LC_MESSAGES/R-KernSmooth.mo
lib/R/library/MASS/CITATION
lib/R/library/MASS/DESCRIPTION
@@ -158,6 +158,7 @@ lib/R/library/MASS/libs/MASS.so
%%NLS%%lib/R/library/MASS/po/de/LC_MESSAGES/R-MASS.mo
%%NLS%%lib/R/library/MASS/po/en@quot/LC_MESSAGES/R-MASS.mo
%%NLS%%lib/R/library/MASS/po/fr/LC_MESSAGES/R-MASS.mo
+%%NLS%%lib/R/library/MASS/po/ko/LC_MESSAGES/R-MASS.mo
%%NLS%%lib/R/library/MASS/po/pl/LC_MESSAGES/R-MASS.mo
lib/R/library/MASS/scripts/ch01.R
lib/R/library/MASS/scripts/ch02.R
@@ -268,19 +269,6 @@ lib/R/library/base/help/base.rdx
lib/R/library/base/help/paths.rds
lib/R/library/base/html/00Index.html
lib/R/library/base/html/R.css
-%%NLS%%lib/R/library/base/po/da/LC_MESSAGES/R-base.mo
-%%NLS%%lib/R/library/base/po/de/LC_MESSAGES/R-base.mo
-%%NLS%%lib/R/library/base/po/en@quot/LC_MESSAGES/R-base.mo
-%%NLS%%lib/R/library/base/po/fr/LC_MESSAGES/R-base.mo
-%%NLS%%lib/R/library/base/po/it/LC_MESSAGES/R-base.mo
-%%NLS%%lib/R/library/base/po/ja/LC_MESSAGES/R-base.mo
-%%NLS%%lib/R/library/base/po/ko/LC_MESSAGES/R-base.mo
-%%NLS%%lib/R/library/base/po/nn/LC_MESSAGES/R-base.mo
-%%NLS%%lib/R/library/base/po/pl/LC_MESSAGES/R-base.mo
-%%NLS%%lib/R/library/base/po/pt_BR/LC_MESSAGES/R-base.mo
-%%NLS%%lib/R/library/base/po/ru/LC_MESSAGES/R-base.mo
-%%NLS%%lib/R/library/base/po/tr/LC_MESSAGES/R-base.mo
-%%NLS%%lib/R/library/base/po/zh_CN/LC_MESSAGES/R-base.mo
lib/R/library/boot/CITATION
lib/R/library/boot/DESCRIPTION
lib/R/library/boot/INDEX
@@ -307,6 +295,7 @@ lib/R/library/boot/html/R.css
%%NLS%%lib/R/library/boot/po/de/LC_MESSAGES/R-boot.mo
%%NLS%%lib/R/library/boot/po/en@quot/LC_MESSAGES/R-boot.mo
%%NLS%%lib/R/library/boot/po/fr/LC_MESSAGES/R-boot.mo
+%%NLS%%lib/R/library/boot/po/ko/LC_MESSAGES/R-boot.mo
%%NLS%%lib/R/library/boot/po/pl/LC_MESSAGES/R-boot.mo
%%NLS%%lib/R/library/boot/po/ru/LC_MESSAGES/R-boot.mo
lib/R/library/class/CITATION
@@ -334,6 +323,7 @@ lib/R/library/class/libs/class.so
%%NLS%%lib/R/library/class/po/de/LC_MESSAGES/R-class.mo
%%NLS%%lib/R/library/class/po/en@quot/LC_MESSAGES/R-class.mo
%%NLS%%lib/R/library/class/po/fr/LC_MESSAGES/R-class.mo
+%%NLS%%lib/R/library/class/po/ko/LC_MESSAGES/R-class.mo
%%NLS%%lib/R/library/class/po/pl/LC_MESSAGES/R-class.mo
lib/R/library/cluster/CITATION
lib/R/library/cluster/DESCRIPTION
@@ -398,16 +388,6 @@ lib/R/library/compiler/help/compiler.rdx
lib/R/library/compiler/help/paths.rds
lib/R/library/compiler/html/00Index.html
lib/R/library/compiler/html/R.css
-%%NLS%%lib/R/library/compiler/po/da/LC_MESSAGES/R-compiler.mo
-%%NLS%%lib/R/library/compiler/po/de/LC_MESSAGES/R-compiler.mo
-%%NLS%%lib/R/library/compiler/po/en@quot/LC_MESSAGES/R-compiler.mo
-%%NLS%%lib/R/library/compiler/po/fr/LC_MESSAGES/R-compiler.mo
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lib/R/library/datasets/DESCRIPTION
lib/R/library/datasets/INDEX
lib/R/library/datasets/Meta/Rd.rds
@@ -431,7 +411,6 @@ lib/R/library/datasets/html/R.css
lib/R/library/foreign/COPYRIGHTS
lib/R/library/foreign/DESCRIPTION
lib/R/library/foreign/INDEX
-lib/R/library/foreign/LICENCE
lib/R/library/foreign/Meta/Rd.rds
lib/R/library/foreign/Meta/hsearch.rds
lib/R/library/foreign/Meta/links.rds
@@ -463,6 +442,7 @@ lib/R/library/foreign/libs/foreign.so
lib/R/library/grDevices/DESCRIPTION
lib/R/library/grDevices/INDEX
lib/R/library/grDevices/Meta/Rd.rds
+lib/R/library/grDevices/Meta/demo.rds
lib/R/library/grDevices/Meta/hsearch.rds
lib/R/library/grDevices/Meta/links.rds
lib/R/library/grDevices/Meta/nsInfo.rds
@@ -560,6 +540,8 @@ lib/R/library/grDevices/afm/tib_____.afm.gz
lib/R/library/grDevices/afm/tibi____.afm.gz
lib/R/library/grDevices/afm/tii_____.afm.gz
lib/R/library/grDevices/afm/tir_____.afm.gz
+lib/R/library/grDevices/demo/colors.R
+lib/R/library/grDevices/demo/hclColors.R
lib/R/library/grDevices/enc/AdobeStd.enc
lib/R/library/grDevices/enc/AdobeSym.enc
lib/R/library/grDevices/enc/CP1250.enc
@@ -589,30 +571,6 @@ lib/R/library/grDevices/icc/srgb
lib/R/library/grDevices/icc/srgb.flate
%%PANGOCAIRO%%lib/R/library/grDevices/libs/cairo.so
lib/R/library/grDevices/libs/grDevices.so
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-%%NLS%%lib/R/library/grDevices/po/da/LC_MESSAGES/grDevices.mo
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-%%NLS%%lib/R/library/grDevices/po/en@quot/LC_MESSAGES/grDevices.mo
-%%NLS%%lib/R/library/grDevices/po/fr/LC_MESSAGES/R-grDevices.mo
-%%NLS%%lib/R/library/grDevices/po/fr/LC_MESSAGES/grDevices.mo
-%%NLS%%lib/R/library/grDevices/po/it/LC_MESSAGES/R-grDevices.mo
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-%%NLS%%lib/R/library/grDevices/po/ja/LC_MESSAGES/R-grDevices.mo
-%%NLS%%lib/R/library/grDevices/po/ja/LC_MESSAGES/grDevices.mo
-%%NLS%%lib/R/library/grDevices/po/ko/LC_MESSAGES/R-grDevices.mo
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-%%NLS%%lib/R/library/grDevices/po/zh_CN/LC_MESSAGES/R-grDevices.mo
-%%NLS%%lib/R/library/grDevices/po/zh_CN/LC_MESSAGES/grDevices.mo
lib/R/library/graphics/DESCRIPTION
lib/R/library/graphics/INDEX
lib/R/library/graphics/Meta/Rd.rds
@@ -645,17 +603,7 @@ lib/R/library/graphics/help/graphics.rdx
lib/R/library/graphics/help/paths.rds
lib/R/library/graphics/html/00Index.html
lib/R/library/graphics/html/R.css
-%%NLS%%lib/R/library/graphics/po/da/LC_MESSAGES/R-graphics.mo
-%%NLS%%lib/R/library/graphics/po/de/LC_MESSAGES/R-graphics.mo
-%%NLS%%lib/R/library/graphics/po/en@quot/LC_MESSAGES/R-graphics.mo
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-%%NLS%%lib/R/library/graphics/po/ja/LC_MESSAGES/R-graphics.mo
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-%%NLS%%lib/R/library/graphics/po/ru/LC_MESSAGES/R-graphics.mo
-%%NLS%%lib/R/library/graphics/po/zh_CN/LC_MESSAGES/R-graphics.mo
+lib/R/library/graphics/libs/graphics.so
lib/R/library/grid/DESCRIPTION
lib/R/library/grid/INDEX
lib/R/library/grid/Meta/Rd.rds
@@ -689,31 +637,9 @@ lib/R/library/grid/help/paths.rds
lib/R/library/grid/html/00Index.html
lib/R/library/grid/html/R.css
lib/R/library/grid/libs/grid.so
-%%NLS%%lib/R/library/grid/po/da/LC_MESSAGES/R-grid.mo
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lib/R/library/lattice/CITATION
lib/R/library/lattice/DESCRIPTION
lib/R/library/lattice/INDEX
-lib/R/library/lattice/LICENSE
lib/R/library/lattice/Meta/Rd.rds
lib/R/library/lattice/Meta/data.rds
lib/R/library/lattice/Meta/demo.rds
@@ -763,26 +689,6 @@ lib/R/library/methods/help/paths.rds
lib/R/library/methods/html/00Index.html
lib/R/library/methods/html/R.css
lib/R/library/methods/libs/methods.so
-%%NLS%%lib/R/library/methods/po/da/LC_MESSAGES/R-methods.mo
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lib/R/library/mgcv/CITATION
lib/R/library/mgcv/DESCRIPTION
lib/R/library/mgcv/INDEX
@@ -875,6 +781,7 @@ lib/R/library/nnet/libs/nnet.so
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%%NLS%%lib/R/library/nnet/po/fr/LC_MESSAGES/R-nnet.mo
+%%NLS%%lib/R/library/nnet/po/ko/LC_MESSAGES/R-nnet.mo
%%NLS%%lib/R/library/nnet/po/pl/LC_MESSAGES/R-nnet.mo
lib/R/library/parallel/DESCRIPTION
lib/R/library/parallel/INDEX
@@ -896,22 +803,6 @@ lib/R/library/parallel/help/paths.rds
lib/R/library/parallel/html/00Index.html
lib/R/library/parallel/html/R.css
lib/R/library/parallel/libs/parallel.so
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lib/R/library/rpart/DESCRIPTION
lib/R/library/rpart/INDEX
lib/R/library/rpart/NEWS.Rd
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%%NLS%%lib/R/library/rpart/po/fr/LC_MESSAGES/rpart.mo
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%%NLS%%lib/R/library/rpart/po/pl/LC_MESSAGES/R-rpart.mo
%%NLS%%lib/R/library/rpart/po/pl/LC_MESSAGES/rpart.mo
%%NLS%%lib/R/library/rpart/po/ru/LC_MESSAGES/R-rpart.mo
@@ -1024,26 +917,6 @@ lib/R/library/splines/help/splines.rdx
lib/R/library/splines/html/00Index.html
lib/R/library/splines/html/R.css
lib/R/library/splines/libs/splines.so
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lib/R/library/stats4/DESCRIPTION
lib/R/library/stats4/INDEX
lib/R/library/stats4/Meta/Rd.rds
@@ -1062,18 +935,6 @@ lib/R/library/stats4/help/stats4.rdb
lib/R/library/stats4/help/stats4.rdx
lib/R/library/stats4/html/00Index.html
lib/R/library/stats4/html/R.css
-%%NLS%%lib/R/library/stats4/po/da/LC_MESSAGES/R-stats4.mo
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+%%NLS%%lib/R/library/translations/pl/LC_MESSAGES/utils.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/R-base.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/R-compiler.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/R-grDevices.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/R-graphics.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/R-grid.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/R-methods.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/R-splines.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/R-stats.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/R-stats4.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/R-tcltk.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/R-tools.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/R-utils.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/R.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/RGui.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/grDevices.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/graphics.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/grid.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/methods.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/splines.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/stats.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/tcltk.mo
+%%NLS%%lib/R/library/translations/pt_BR/LC_MESSAGES/tools.mo
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+%%NLS%%lib/R/library/translations/ru/LC_MESSAGES/R-grDevices.mo
+%%NLS%%lib/R/library/translations/ru/LC_MESSAGES/R-graphics.mo
+%%NLS%%lib/R/library/translations/ru/LC_MESSAGES/R-grid.mo
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+%%NLS%%lib/R/library/translations/ru/LC_MESSAGES/R-tcltk.mo
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+%%NLS%%lib/R/library/translations/ru/LC_MESSAGES/stats.mo
+%%NLS%%lib/R/library/translations/ru/LC_MESSAGES/tcltk.mo
+%%NLS%%lib/R/library/translations/ru/LC_MESSAGES/tools.mo
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+%%NLS%%lib/R/library/translations/tr/LC_MESSAGES/R-stats.mo
+%%NLS%%lib/R/library/translations/tr/LC_MESSAGES/R-stats4.mo
+%%NLS%%lib/R/library/translations/tr/LC_MESSAGES/R-tools.mo
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+%%NLS%%lib/R/library/translations/tr/LC_MESSAGES/R.mo
+%%NLS%%lib/R/library/translations/tr/LC_MESSAGES/RGui.mo
+%%NLS%%lib/R/library/translations/tr/LC_MESSAGES/graphics.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-base.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-compiler.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-grDevices.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-graphics.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-grid.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-methods.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-parallel.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-splines.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-stats.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-stats4.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-tcltk.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-tools.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R-utils.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/R.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/RGui.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/grDevices.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/graphics.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/grid.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/methods.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/parallel.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/splines.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/stats.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/tcltk.mo
+%%NLS%%lib/R/library/translations/zh_CN/LC_MESSAGES/tools.mo
+%%NLS%%lib/R/library/translations/zh_TW/LC_MESSAGES/R.mo
+%%NLS%%lib/R/library/translations/zh_TW/LC_MESSAGES/RGui.mo
+%%NLS%%lib/R/library/translations/zh_TW/LC_MESSAGES/graphics.mo
lib/R/library/utils/DESCRIPTION
lib/R/library/utils/INDEX
lib/R/library/utils/Meta/Rd.rds
@@ -1276,20 +1348,11 @@ lib/R/library/utils/help/utils.rdx
lib/R/library/utils/html/00Index.html
lib/R/library/utils/html/R.css
lib/R/library/utils/iconvlist
+lib/R/library/utils/libs/utils.so
lib/R/library/utils/misc/exDIF.csv
lib/R/library/utils/misc/exDIF.dif
-%%NLS%%lib/R/library/utils/po/da/LC_MESSAGES/R-utils.mo
-%%NLS%%lib/R/library/utils/po/de/LC_MESSAGES/R-utils.mo
-%%NLS%%lib/R/library/utils/po/en@quot/LC_MESSAGES/R-utils.mo
-%%NLS%%lib/R/library/utils/po/fr/LC_MESSAGES/R-utils.mo
-%%NLS%%lib/R/library/utils/po/ja/LC_MESSAGES/R-utils.mo
-%%NLS%%lib/R/library/utils/po/ko/LC_MESSAGES/R-utils.mo
-%%NLS%%lib/R/library/utils/po/pl/LC_MESSAGES/R-utils.mo
-%%NLS%%lib/R/library/utils/po/pt_BR/LC_MESSAGES/R-utils.mo
-%%NLS%%lib/R/library/utils/po/ru/LC_MESSAGES/R-utils.mo
-%%NLS%%lib/R/library/utils/po/tr/LC_MESSAGES/R-utils.mo
-%%NLS%%lib/R/library/utils/po/zh_CN/LC_MESSAGES/R-utils.mo
%%X11%%lib/R/modules/R_X11.so
+%%X11%%lib/R/modules/R_de.so
lib/R/modules/internet.so
lib/R/modules/lapack.so
lib/R/modules/vfonts.so
@@ -1298,36 +1361,22 @@ lib/R/share/R/examples-footer.R
lib/R/share/R/examples-header.R
lib/R/share/R/nspackloader.R
lib/R/share/R/tests-startup.R
+lib/R/share/dictionaries/en_stats.rds
lib/R/share/encodings/Adobe-glyphlist
lib/R/share/encodings/character-sets
lib/R/share/java/README
lib/R/share/java/getsp.class
lib/R/share/licenses/AGPL-3
-lib/R/share/licenses/Artistic-1.0
lib/R/share/licenses/Artistic-2.0
+lib/R/share/licenses/BSD_2_clause
+lib/R/share/licenses/BSD_3_clause
lib/R/share/licenses/GPL-2
lib/R/share/licenses/GPL-3
lib/R/share/licenses/LGPL-2
lib/R/share/licenses/LGPL-2.1
lib/R/share/licenses/LGPL-3
+lib/R/share/licenses/MIT
lib/R/share/licenses/license.db
-%%NLS%%lib/R/share/locale/da/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/de/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/en_GB/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/en/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/en@quot/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/es/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/fr/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/it/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/ja/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/ko/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/nn/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/pl/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/pt_BR/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/ru/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/tr/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/zh_CN/LC_MESSAGES/R.mo
-%%NLS%%lib/R/share/locale/zh_TW/LC_MESSAGES/R.mo
lib/R/share/make/basepkg.mk
lib/R/share/make/check.mk
lib/R/share/make/clean.mk
@@ -1373,71 +1422,15 @@ lib/R/share/texmf/tex/latex/upquote.sty
@dirrm lib/R/share/texmf
@dirrm lib/R/share/sh
@dirrm lib/R/share/make
-%%NLS%%@dirrm lib/R/share/locale/zh_TW/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/zh_TW
-%%NLS%%@dirrm lib/R/share/locale/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/zh_CN
-%%NLS%%@dirrm lib/R/share/locale/tr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/tr
-%%NLS%%@dirrm lib/R/share/locale/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/ru
-%%NLS%%@dirrm lib/R/share/locale/pt_BR/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/pt_BR
-%%NLS%%@dirrm lib/R/share/locale/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/pl
-%%NLS%%@dirrm lib/R/share/locale/nn/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/nn
-%%NLS%%@dirrm lib/R/share/locale/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/ko
-%%NLS%%@dirrm lib/R/share/locale/ja/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/ja
-%%NLS%%@dirrm lib/R/share/locale/it/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/it
-%%NLS%%@dirrm lib/R/share/locale/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/fr
-%%NLS%%@dirrm lib/R/share/locale/es/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/es
-%%NLS%%@dirrm lib/R/share/locale/en@quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/en@quot
-%%NLS%%@dirrm lib/R/share/locale/en/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/en_GB/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/en_GB
-%%NLS%%@dirrm lib/R/share/locale/en
-%%NLS%%@dirrm lib/R/share/locale/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/de
-%%NLS%%@dirrm lib/R/share/locale/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/share/locale/da
-%%NLS%%@dirrm lib/R/share/locale
@dirrm lib/R/share/licenses
@dirrm lib/R/share/java
@dirrm lib/R/share/encodings
+@dirrm lib/R/share/dictionaries
@dirrm lib/R/share/R
@dirrm lib/R/share
@dirrm lib/R/modules
-%%NLS%%@dirrm lib/R/library/utils/po/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/utils/po/zh_CN
-%%NLS%%@dirrm lib/R/library/utils/po/tr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/utils/po/tr
-%%NLS%%@dirrm lib/R/library/utils/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/utils/po/ru
-%%NLS%%@dirrm lib/R/library/utils/po/pt_BR/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/utils/po/pt_BR
-%%NLS%%@dirrm lib/R/library/utils/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/utils/po/pl
-%%NLS%%@dirrm lib/R/library/utils/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/utils/po/ko
-%%NLS%%@dirrm lib/R/library/utils/po/ja/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/utils/po/ja
-%%NLS%%@dirrm lib/R/library/utils/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/utils/po/fr
-%%NLS%%@dirrm lib/R/library/utils/po/en@quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/utils/po/en@quot
-%%NLS%%@dirrm lib/R/library/utils/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/utils/po/de
-%%NLS%%@dirrm lib/R/library/utils/po/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/utils/po/da
-%%NLS%%@dirrm lib/R/library/utils/po
@dirrm lib/R/library/utils/misc
+@dirrm lib/R/library/utils/libs
@dirrm lib/R/library/utils/html
@dirrm lib/R/library/utils/help
@dirrm lib/R/library/utils/doc
@@ -1445,60 +1438,49 @@ lib/R/share/texmf/tex/latex/upquote.sty
@dirrm lib/R/library/utils/R
@dirrm lib/R/library/utils/Meta
@dirrm lib/R/library/utils
-%%NLS%%@dirrm lib/R/library/tools/po/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tools/po/zh_CN
-%%NLS%%@dirrm lib/R/library/tools/po/tr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tools/po/tr
-%%NLS%%@dirrm lib/R/library/tools/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tools/po/ru
-%%NLS%%@dirrm lib/R/library/tools/po/pt_BR/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tools/po/pt_BR
-%%NLS%%@dirrm lib/R/library/tools/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tools/po/pl
-%%NLS%%@dirrm lib/R/library/tools/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tools/po/ko
-%%NLS%%@dirrm lib/R/library/tools/po/ja/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tools/po/ja
-%%NLS%%@dirrm lib/R/library/tools/po/it/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tools/po/it
-%%NLS%%@dirrm lib/R/library/tools/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tools/po/fr
-%%NLS%%@dirrm lib/R/library/tools/po/en@quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tools/po/en@quot
-%%NLS%%@dirrm lib/R/library/tools/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tools/po/de
-%%NLS%%@dirrm lib/R/library/tools/po/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tools/po/da
-%%NLS%%@dirrm lib/R/library/tools/po
+%%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@quot/LC_MESSAGES
+%%NLS%%@dirrm lib/R/library/translations/en@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
+@dirrm lib/R/library/translations
@dirrm lib/R/library/tools/libs
@dirrm lib/R/library/tools/html
@dirrm lib/R/library/tools/help
@dirrm lib/R/library/tools/R
@dirrm lib/R/library/tools/Meta
@dirrm lib/R/library/tools
-%%NLS%%@dirrm lib/R/library/tcltk/po/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tcltk/po/zh_CN
-%%NLS%%@dirrm lib/R/library/tcltk/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tcltk/po/ru
-%%NLS%%@dirrm lib/R/library/tcltk/po/pt_BR/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tcltk/po/pt_BR
-%%NLS%%@dirrm lib/R/library/tcltk/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tcltk/po/pl
-%%NLS%%@dirrm lib/R/library/tcltk/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tcltk/po/ko
-%%NLS%%@dirrm lib/R/library/tcltk/po/ja/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tcltk/po/ja
-%%NLS%%@dirrm lib/R/library/tcltk/po/it/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tcltk/po/it
-%%NLS%%@dirrm lib/R/library/tcltk/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tcltk/po/fr
-%%NLS%%@dirrm lib/R/library/tcltk/po/en@quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tcltk/po/en@quot
-%%NLS%%@dirrm lib/R/library/tcltk/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tcltk/po/de
-%%NLS%%@dirrm lib/R/library/tcltk/po/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/tcltk/po/da
-%%NLS%%@dirrm lib/R/library/tcltk/po
%%TCLTK%%@dirrm lib/R/library/tcltk/libs
@dirrm lib/R/library/tcltk/html
@dirrm lib/R/library/tcltk/help
@@ -1515,89 +1497,18 @@ lib/R/share/texmf/tex/latex/upquote.sty
@dirrm lib/R/library/survival/R
@dirrm lib/R/library/survival/Meta
@dirrm lib/R/library/survival
-%%NLS%%@dirrm lib/R/library/stats/po/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats/po/zh_CN
-%%NLS%%@dirrm lib/R/library/stats/po/tr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats/po/tr
-%%NLS%%@dirrm lib/R/library/stats/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats/po/ru
-%%NLS%%@dirrm lib/R/library/stats/po/pt_BR/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats/po/pt_BR
-%%NLS%%@dirrm lib/R/library/stats/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats/po/pl
-%%NLS%%@dirrm lib/R/library/stats/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats/po/ko
-%%NLS%%@dirrm lib/R/library/stats/po/ja/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats/po/ja
-%%NLS%%@dirrm lib/R/library/stats/po/it/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats/po/it
-%%NLS%%@dirrm lib/R/library/stats/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats/po/fr
-%%NLS%%@dirrm lib/R/library/stats/po/en@quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats/po/en@quot
-%%NLS%%@dirrm lib/R/library/stats/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats/po/de
-%%NLS%%@dirrm lib/R/library/stats/po/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats/po/da
-%%NLS%%@dirrm lib/R/library/stats/po
@dirrm lib/R/library/stats/libs
@dirrm lib/R/library/stats/html
@dirrm lib/R/library/stats/help
@dirrm lib/R/library/stats/demo
@dirrm lib/R/library/stats/R
@dirrm lib/R/library/stats/Meta
-%%NLS%%@dirrm lib/R/library/stats4/po/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats4/po/zh_CN
-%%NLS%%@dirrm lib/R/library/stats4/po/tr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats4/po/tr
-%%NLS%%@dirrm lib/R/library/stats4/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats4/po/ru
-%%NLS%%@dirrm lib/R/library/stats4/po/pt_BR/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats4/po/pt_BR
-%%NLS%%@dirrm lib/R/library/stats4/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats4/po/pl
-%%NLS%%@dirrm lib/R/library/stats4/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats4/po/ko
-%%NLS%%@dirrm lib/R/library/stats4/po/ja/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats4/po/ja
-%%NLS%%@dirrm lib/R/library/stats4/po/it/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats4/po/it
-%%NLS%%@dirrm lib/R/library/stats4/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats4/po/fr
-%%NLS%%@dirrm lib/R/library/stats4/po/en@quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats4/po/en@quot
-%%NLS%%@dirrm lib/R/library/stats4/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats4/po/de
-%%NLS%%@dirrm lib/R/library/stats4/po/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/stats4/po/da
-%%NLS%%@dirrm lib/R/library/stats4/po
@dirrm lib/R/library/stats4/html
@dirrm lib/R/library/stats4/help
@dirrm lib/R/library/stats4/R
@dirrm lib/R/library/stats4/Meta
@dirrm lib/R/library/stats4
@dirrm lib/R/library/stats
-%%NLS%%@dirrm lib/R/library/splines/po/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/splines/po/zh_CN
-%%NLS%%@dirrm lib/R/library/splines/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/splines/po/ru
-%%NLS%%@dirrm lib/R/library/splines/po/pt_BR/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/splines/po/pt_BR
-%%NLS%%@dirrm lib/R/library/splines/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/splines/po/pl
-%%NLS%%@dirrm lib/R/library/splines/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/splines/po/ko
-%%NLS%%@dirrm lib/R/library/splines/po/ja/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/splines/po/ja
-%%NLS%%@dirrm lib/R/library/splines/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/splines/po/fr
-%%NLS%%@dirrm lib/R/library/splines/po/en@quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/splines/po/en@quot
-%%NLS%%@dirrm lib/R/library/splines/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/splines/po/de
-%%NLS%%@dirrm lib/R/library/splines/po/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/splines/po/da
-%%NLS%%@dirrm lib/R/library/splines/po
@dirrm lib/R/library/splines/libs
@dirrm lib/R/library/splines/html
@dirrm lib/R/library/splines/help
@@ -1624,6 +1535,8 @@ lib/R/share/texmf/tex/latex/upquote.sty
%%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@quot/LC_MESSAGES
@@ -1639,23 +1552,6 @@ lib/R/share/texmf/tex/latex/upquote.sty
@dirrm lib/R/library/rpart/R
@dirrm lib/R/library/rpart/Meta
@dirrm lib/R/library/rpart
-%%NLS%%@dirrm lib/R/library/parallel/po/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/parallel/po/zh_CN
-%%NLS%%@dirrm lib/R/library/parallel/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/parallel/po/ru
-%%NLS%%@dirrm lib/R/library/parallel/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/parallel/po/pl
-%%NLS%%@dirrm lib/R/library/parallel/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/parallel/po/ko
-%%NLS%%@dirrm lib/R/library/parallel/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/parallel/po/fr
-%%NLS%%@dirrm lib/R/library/parallel/po/en@quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/parallel/po/en@quot
-%%NLS%%@dirrm lib/R/library/parallel/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/parallel/po/de
-%%NLS%%@dirrm lib/R/library/parallel/po/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/parallel/po/da
-%%NLS%%@dirrm lib/R/library/parallel/po
@dirrm lib/R/library/parallel/libs
@dirrm lib/R/library/parallel/html
@dirrm lib/R/library/parallel/help
@@ -1665,6 +1561,8 @@ lib/R/share/texmf/tex/latex/upquote.sty
@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@quot/LC_MESSAGES
@@ -1703,27 +1601,6 @@ lib/R/share/texmf/tex/latex/upquote.sty
@dirrm lib/R/library/mgcv/R
@dirrm lib/R/library/mgcv/Meta
@dirrm lib/R/library/mgcv
-%%NLS%%@dirrm lib/R/library/methods/po/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/methods/po/zh_CN
-%%NLS%%@dirrm lib/R/library/methods/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/methods/po/ru
-%%NLS%%@dirrm lib/R/library/methods/po/pt_BR/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/methods/po/pt_BR
-%%NLS%%@dirrm lib/R/library/methods/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/methods/po/pl
-%%NLS%%@dirrm lib/R/library/methods/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/methods/po/ko
-%%NLS%%@dirrm lib/R/library/methods/po/ja/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/methods/po/ja
-%%NLS%%@dirrm lib/R/library/methods/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/methods/po/fr
-%%NLS%%@dirrm lib/R/library/methods/po/en@quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/methods/po/en@quot
-%%NLS%%@dirrm lib/R/library/methods/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/methods/po/de
-%%NLS%%@dirrm lib/R/library/methods/po/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/methods/po/da
-%%NLS%%@dirrm lib/R/library/methods/po
@dirrm lib/R/library/methods/libs
@dirrm lib/R/library/methods/html
@dirrm lib/R/library/methods/help
@@ -1745,29 +1622,6 @@ lib/R/share/texmf/tex/latex/upquote.sty
@dirrm lib/R/library/lattice/R
@dirrm lib/R/library/lattice/Meta
@dirrm lib/R/library/lattice
-%%NLS%%@dirrm lib/R/library/grid/po/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grid/po/zh_CN
-%%NLS%%@dirrm lib/R/library/grid/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grid/po/ru
-%%NLS%%@dirrm lib/R/library/grid/po/pt_BR/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grid/po/pt_BR
-%%NLS%%@dirrm lib/R/library/grid/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grid/po/pl
-%%NLS%%@dirrm lib/R/library/grid/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grid/po/ko
-%%NLS%%@dirrm lib/R/library/grid/po/ja/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grid/po/ja
-%%NLS%%@dirrm lib/R/library/grid/po/it/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grid/po/it
-%%NLS%%@dirrm lib/R/library/grid/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grid/po/fr
-%%NLS%%@dirrm lib/R/library/grid/po/en@quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grid/po/en@quot
-%%NLS%%@dirrm lib/R/library/grid/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grid/po/de
-%%NLS%%@dirrm lib/R/library/grid/po/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grid/po/da
-%%NLS%%@dirrm lib/R/library/grid/po
@dirrm lib/R/library/grid/libs
@dirrm lib/R/library/grid/html
@dirrm lib/R/library/grid/help
@@ -1775,29 +1629,7 @@ lib/R/share/texmf/tex/latex/upquote.sty
@dirrm lib/R/library/grid/R
@dirrm lib/R/library/grid/Meta
@dirrm lib/R/library/grid
-%%NLS%%@dirrm lib/R/library/graphics/po/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/graphics/po/zh_CN
-%%NLS%%@dirrm lib/R/library/graphics/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/graphics/po/ru
-%%NLS%%@dirrm lib/R/library/graphics/po/pt_BR/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/graphics/po/pt_BR
-%%NLS%%@dirrm lib/R/library/graphics/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/graphics/po/pl
-%%NLS%%@dirrm lib/R/library/graphics/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/graphics/po/ko
-%%NLS%%@dirrm lib/R/library/graphics/po/ja/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/graphics/po/ja
-%%NLS%%@dirrm lib/R/library/graphics/po/it/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/graphics/po/it
-%%NLS%%@dirrm lib/R/library/graphics/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/graphics/po/fr
-%%NLS%%@dirrm lib/R/library/graphics/po/en@quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/graphics/po/en@quot
-%%NLS%%@dirrm lib/R/library/graphics/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/graphics/po/de
-%%NLS%%@dirrm lib/R/library/graphics/po/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/graphics/po/da
-%%NLS%%@dirrm lib/R/library/graphics/po
+@dirrm lib/R/library/graphics/libs
@dirrm lib/R/library/graphics/html
@dirrm lib/R/library/graphics/help/figures
@dirrm lib/R/library/graphics/help
@@ -1805,36 +1637,12 @@ lib/R/share/texmf/tex/latex/upquote.sty
@dirrm lib/R/library/graphics/R
@dirrm lib/R/library/graphics/Meta
@dirrm lib/R/library/graphics
-%%NLS%%@dirrm lib/R/library/grDevices/po/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grDevices/po/zh_CN
-%%NLS%%@dirrm lib/R/library/grDevices/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grDevices/po/ru
-%%NLS%%@dirrm lib/R/library/grDevices/po/pt_BR/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grDevices/po/pt_BR
-%%NLS%%@dirrm lib/R/library/grDevices/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grDevices/po/pl
-%%NLS%%@dirrm lib/R/library/grDevices/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grDevices/po/ko
-%%NLS%%@dirrm lib/R/library/grDevices/po/ja/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grDevices/po/ja
-%%NLS%%@dirrm lib/R/library/grDevices/po/it/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grDevices/po/it
-%%NLS%%@dirrm lib/R/library/grDevices/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grDevices/po/fr
-%%NLS%%@dirrm lib/R/library/grDevices/po/en@quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grDevices/po/en@quot
-%%NLS%%@dirrm lib/R/library/grDevices/po/en_GB/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grDevices/po/en_GB
-%%NLS%%@dirrm lib/R/library/grDevices/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grDevices/po/de
-%%NLS%%@dirrm lib/R/library/grDevices/po/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/grDevices/po/da
-%%NLS%%@dirrm lib/R/library/grDevices/po
@dirrm lib/R/library/grDevices/libs
@dirrm lib/R/library/grDevices/icc
@dirrm lib/R/library/grDevices/html
@dirrm lib/R/library/grDevices/help
@dirrm lib/R/library/grDevices/enc
+@dirrm lib/R/library/grDevices/demo
@dirrm lib/R/library/grDevices/afm
@dirrm lib/R/library/grDevices/R
@dirrm lib/R/library/grDevices/Meta
@@ -1860,27 +1668,6 @@ lib/R/share/texmf/tex/latex/upquote.sty
@dirrm lib/R/library/datasets/data
@dirrm lib/R/library/datasets/Meta
@dirrm lib/R/library/datasets
-%%NLS%%@dirrm lib/R/library/compiler/po/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/compiler/po/zh_CN
-%%NLS%%@dirrm lib/R/library/compiler/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/compiler/po/ru
-%%NLS%%@dirrm lib/R/library/compiler/po/pt_BR/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/compiler/po/pt_BR
-%%NLS%%@dirrm lib/R/library/compiler/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/compiler/po/pl
-%%NLS%%@dirrm lib/R/library/compiler/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/compiler/po/ko
-%%NLS%%@dirrm lib/R/library/compiler/po/ja/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/compiler/po/ja
-%%NLS%%@dirrm lib/R/library/compiler/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/compiler/po/fr
-%%NLS%%@dirrm lib/R/library/compiler/po/en@quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/compiler/po/en@quot
-%%NLS%%@dirrm lib/R/library/compiler/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/compiler/po/de
-%%NLS%%@dirrm lib/R/library/compiler/po/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/compiler/po/da
-%%NLS%%@dirrm lib/R/library/compiler/po
@dirrm lib/R/library/compiler/html
@dirrm lib/R/library/compiler/help
@dirrm lib/R/library/compiler/R
@@ -1907,6 +1694,8 @@ lib/R/share/texmf/tex/latex/upquote.sty
@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@quot/LC_MESSAGES
@@ -1924,6 +1713,8 @@ lib/R/share/texmf/tex/latex/upquote.sty
%%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@quot/LC_MESSAGES
@@ -1937,33 +1728,6 @@ lib/R/share/texmf/tex/latex/upquote.sty
@dirrm lib/R/library/boot/R
@dirrm lib/R/library/boot/Meta
@dirrm lib/R/library/boot
-%%NLS%%@dirrm lib/R/library/base/po/zh_CN/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/base/po/zh_CN
-%%NLS%%@dirrm lib/R/library/base/po/tr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/base/po/tr
-%%NLS%%@dirrm lib/R/library/base/po/ru/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/base/po/ru
-%%NLS%%@dirrm lib/R/library/base/po/pt_BR/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/base/po/pt_BR
-%%NLS%%@dirrm lib/R/library/base/po/pl/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/base/po/pl
-%%NLS%%@dirrm lib/R/library/base/po/nn/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/base/po/nn
-%%NLS%%@dirrm lib/R/library/base/po/ko/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/base/po/ko
-%%NLS%%@dirrm lib/R/library/base/po/ja/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/base/po/ja
-%%NLS%%@dirrm lib/R/library/base/po/it/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/base/po/it
-%%NLS%%@dirrm lib/R/library/base/po/fr/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/base/po/fr
-%%NLS%%@dirrm lib/R/library/base/po/en@quot/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/base/po/en@quot
-%%NLS%%@dirrm lib/R/library/base/po/de/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/base/po/de
-%%NLS%%@dirrm lib/R/library/base/po/da/LC_MESSAGES
-%%NLS%%@dirrm lib/R/library/base/po/da
-%%NLS%%@dirrm lib/R/library/base/po
@dirrm lib/R/library/base/html
@dirrm lib/R/library/base/help
@dirrm lib/R/library/base/demo
@@ -1991,6 +1755,8 @@ lib/R/share/texmf/tex/latex/upquote.sty
@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@quot/LC_MESSAGES
@@ -2007,6 +1773,8 @@ lib/R/share/texmf/tex/latex/upquote.sty
@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@quot/LC_MESSAGES
%%NLS%%@dirrm lib/R/library/KernSmooth/po/en@quot
%%NLS%%@dirrm lib/R/library/KernSmooth/po/de/LC_MESSAGES
generated by cgit (git 2.34.1) at 2024-11-15 22:51:01 +0800