diff options
Diffstat (limited to 'math/R/files/patch-20130526')
| -rw-r--r-- | math/R/files/patch-20130526 | 2831 |
1 files changed, 0 insertions, 2831 deletions
diff --git a/math/R/files/patch-20130526 b/math/R/files/patch-20130526 deleted file mode 100644 index 5f3c74252ae9..000000000000 --- a/math/R/files/patch-20130526 +++ /dev/null @@ -1,2831 +0,0 @@ -diff -ruN R-3.0.1/NEWS R-patched/NEWS ---- NEWS 2013-05-16 03:05:47.000000000 -0400 -+++ NEWS 2013-05-26 18:10:19.000000000 -0400 -@@ -1,5 +1,44 @@ - R News - -+CHANGES IN R 3.0.1 patched: -+ -+ NEW FEATURES: -+ -+ o The macros used for the texinfo manuals have been changed to work -+ better with the incompatible changes made in texinfo 5.x. -+ -+ o The example() and tools::Rd2ex() functions now have parameters to -+ allow them to ignore \dontrun markup in examples. (Suggested by -+ Peter Solymos.) -+ -+ C-LEVEL FACILITIES: -+ -+ o Rdefines.h has been tweaked so it can be included in C++ code -+ with R_exts/Boolean.h (which is included by R.h). Note though -+ that Rdefines.h is not kept up-to-date, and Rinternals.h is -+ preferred for new code. -+ -+ BUG FIXES: -+ -+ o help.request() could not determine the current version of R on -+ CRAN. (PR#15241) -+ -+ o On Windows, file.info() failed on root directories unless the -+ path was terminated with an explicit ".". (PR#15302) -+ -+ o The regmatches<-() replacement function mishandled results coming -+ from regexpr(). (PR#15311) -+ -+ o Documentation for setClass and representation still suggested the -+ deprecated argument representation=. (PR#15312) -+ -+ o R CMD config failed in an installed build of R 3.0.1 (only) when -+ a sub-architecture was used. (Reported by Berwin Turlach.) -+ -+ o On Windows, the installer modified the etc/Rconsole and -+ etc/Rprofile.site files even when default options were chosen. -+ (Reported by Tal Galili.) -+ - CHANGES IN R 3.0.1: - - NEW FEATURES: -Files R-3.0.1/NEWS.pdf and R-patched/NEWS.pdf differ -diff -ruN R-3.0.1/SVN-REVISION R-patched/SVN-REVISION ---- SVN-REVISION 2013-05-16 03:01:22.000000000 -0400 -+++ SVN-REVISION 2013-05-26 18:06:20.000000000 -0400 -@@ -1,2 +1,2 @@ --Revision: 62743 --Last Changed Date: 2013-05-16 -+Revision: 62815 -+Last Changed Date: 2013-05-26 -diff -ruN R-3.0.1/VERSION R-patched/VERSION ---- VERSION 2013-05-16 03:00:06.000000000 -0400 -+++ VERSION 2013-05-16 03:11:45.000000000 -0400 -@@ -1 +1 @@ --3.0.1 -+3.0.1 Patched -diff -ruN R-3.0.1/doc/CRAN_mirrors.csv R-patched/doc/CRAN_mirrors.csv ---- doc/CRAN_mirrors.csv 2013-04-18 18:05:05.000000000 -0400 -+++ doc/CRAN_mirrors.csv 2013-05-24 18:05:06.000000000 -0400 -@@ -32,7 +32,6 @@ - "France (Paris 2)",France,Paris,http://cran.univ-paris1.fr/,"Universite Paris 1 Pantheon-Sorbonne","pierre.latouche # univ-paris1.fr",1,fr - "Germany (Berlin)",Germany,Berlin,http://mirrors.softliste.de/cran/,"Softliste.de, Berlin","docko # docko.sk",1,de - "Germany (Bonn)",Germany,Bonn,http://cran.r-mirror.de/,"Stefan Drees, Bonn","stefan # drees.name",1,de --"Germany (Falkenstein)",Germany,Falkenstein,http://mirror.layerjet.com/cran,layerjet.com,"Elton Chung <elton # layerjet.com>",1,de - "Germany (Goettingen)",Germany,Goettingen,http://ftp5.gwdg.de/pub/misc/cran/,"GWDG Goettingen","Eberhard Moenkeberg <emoenke # gwdg.de>",1,de - Greece,Greece,Crete,http://cran.cc.uoc.gr/,"University of Crete","mirrors # Cc.uoc.gr",1,gr - Hungary,Hungary,Budapest,http://cran.rapporter.net/,"Rapporter.net, Budapest","Daróczi Gergely <gergely # snowl.net>",1,hu -@@ -48,7 +47,6 @@ - "Japan (Tokyo)",Japan,Tokyo,http://cran.ism.ac.jp/,"Institute of Statistical Mathematics, Tokyo","Junji Nakano <nakanoj # ism.ac.jp>",1,jp - "Korea (Seoul 1)",Korea,Seoul,http://cran.nexr.com/,"NexR Corporation, Seoul","mining # nexr.com",1,kr - "Korea (Seoul 2)",Korea,Seoul,http://biostat.cau.ac.kr/CRAN/,"Chung-Ang University, Seoul","Sunghow # gmail.com",1,kr --Latvia,Latvia,Riga,http://mirrors.webhostinggeeks.com/cran/,Webhostinggeeks,"whg.igp # gmail.com",1,lv - "Mexico (Mexico City)",Mexico,"Mexico City",http://cran.itam.mx/,"Instituto Tecnologico Autonomo de Mexico","Ernesto Barrios <ebarrios # Itam.mx>",1,mx - "Mexico (Texcoco)",Mexico,Texcoco,http://www.est.colpos.mx/R-mirror/,"Colegio de Postgraduados, Texcoco","perpdgo # gmail.com",1,mx - "Netherlands (Amsterdam)",Netherlands,Amsterdam,http://cran.xl-mirror.nl/,"XL-Data, Amsterdam","werner # xl-mirror.nl",1,nl -@@ -57,6 +55,7 @@ - Norway,Norway,Bergen,http://cran.uib.no/,"University of Bergen","sundrift # It.uib.no",1,no - Philippines,Philippines,"Quezon City",http://cran.stat.upd.edu.ph/,"University of the Philippines and PREGINET","edward.p.santos # Up.edu.ph",1,ph - Poland,Poland,Wroclaw,http://r.meteo.uni.wroc.pl/,"University of Wroclaw","Paweł Netzel <netzel # meteo.uni.wroc.pl>",1,pl -+Portugal,Portugal,Porto,http://cran.dcc.fc.up.pt/,"University of Porto","labcc # labcc.dcc.fc.up.pt",1,pt - Russia,Russia,Moscow,http://cran.gis-lab.info/,GIS-Lab.info,"sim # gis-lab.info",1,ru - Singapore,Singapore,Singapore,http://cran.stat.nus.edu.sg/,"National University of Singapore","Zhang Rong <ccezr # nus.edu.sg>",1,sg - Slovakia,Slovakia,Bratislava,http://cran.fyxm.net/,"FYXM.net, Bratislava","docko # docko.sk",1,sk -@@ -74,7 +73,7 @@ - "UK (St Andrews)",UK,"St Andrews",http://star-www.st-andrews.ac.uk/cran/,"St Andrews University","Lee Kelvin <lsk9 # St-andrews.ac.uk>",1,uk - "USA (CA 1)",USA,Berkeley,http://cran.cnr.Berkeley.edu,"University of California, Berkeley, CA","casterln # nature.berkeley.edu",1,us - "USA (CA 2)",USA,"Los Angeles",http://cran.stat.ucla.edu/,"University of California, Los Angeles, CA","Jose Hales-Garcia <jose # stat.ucla.edu>",1,us --"USA (IA)",USA,Ames,http://streaming.stat.iastate.edu/CRAN/,"Iowa State University, Ames, IA","Ted Peterson <statit # iastate.edu>",1,us -+"USA (IA)",USA,Ames,http://streaming.stat.iastate.edu/CRAN/,"Iowa State University, Ames, IA","statit # iastate.edu",1,us - "USA (IN)",USA,Bloomington,http://ftp.ussg.iu.edu/CRAN/,"Indiana University","rtadmin # indiana.edu",1,us - "USA (KS)",USA,Lawrence,http://rweb.quant.ku.edu/cran/,"University of Kansas, Lawrence, KS","Paul Johnson <pauljohn # ku.edu>",1,us - "USA (MD)",USA,Bethesda,http://watson.nci.nih.gov/cran_mirror/,"National Cancer Institute, Bethesda, MD","Sean Davis <sdavis2 # mail.nih.gov>",1,us -diff -ruN R-3.0.1/doc/NEWS.Rd R-patched/doc/NEWS.Rd ---- doc/NEWS.Rd 2013-05-11 18:05:03.000000000 -0400 -+++ doc/NEWS.Rd 2013-05-25 18:05:04.000000000 -0400 -@@ -7,6 +7,53 @@ - \title{ R News} - \encoding{UTF-8} - -+\section{\Rlogo CHANGES IN R 3.0.1 patched}{ -+ \subsection{NEW FEATURES}{ -+ \itemize{ -+ \item The macros used for the texinfo manuals have been changed to -+ work better with the incompatible changes made in texinfo 5.x. -+ -+ \item The \code{example()} and \code{tools::Rd2ex()} functions now -+ have parameters to allow them to ignore \verb{\dontrun} markup in -+ examples. (Suggested by Peter Solymos.) -+ } -+ } -+ -+ \subsection{C-LEVEL FACILITIES}{ -+ \itemize{ -+ \item \file{Rdefines.h} has been tweaked so it can be included in -+ C++ code with \file{R_exts/Boolean.h} (which is included by -+ \file{R.h}). Note though that \file{Rdefines.h} is not kept -+ up-to-date, and \file{Rinternals.h} is preferred for new code. -+ } -+ } -+ -+ \subsection{BUG FIXES}{ -+ \itemize{ -+ \item \code{help.request()} could not determine the current version -+ of \R on CRAN. (\PR{15241}) -+ -+ \item On Windows, \code{file.info()} failed on root directories unless -+ the path was terminated with an explicit \code{"."}. (\PR{15302}) -+ -+ \item The \code{regmatches<-()} replacement function mishandled -+ results coming from \code{regexpr()}. (\PR{15311}) -+ -+ \item Documentation for \code{setClass} and -+ \code{representation} still suggested the deprecated argument -+ \code{representation=}. (\PR{15312}) -+ -+ \item \command{R CMD config} failed in an installed build of \R -+ 3.0.1 (only) when a sub-architecture was used. (Reported by -+ Berwin Turlach.) -+ -+ \item On Windows, the installer modified the \file{etc/Rconsole} and -+ \file{etc/Rprofile.site} files even when default options were -+ chosen. (Reported by Tal Galili.) -+ } -+ } -+} -+ - \section{\Rlogo CHANGES IN R 3.0.1}{ - \subsection{NEW FEATURES}{ - \itemize{ -@@ -142,28 +189,28 @@ - \item \code{as.dendrogram()}'s \code{hclust} method uses less - memory and hence gets considerably faster for large (n ~ 1000) - clusterings, thanks to Daniel Müllner. (\PR{15174}) -- -+ - \item The return value when all workers failed from - \code{parallel::mclapply(mc.presechedule = TRUE)} was a list of - strings and not of error objects. (Spotted by Karl Forner and -- Bernd Bischl.) -- -+ Bernd Bischl.) -+ - \item In \R 3.0.0, when \code{help()} found multiple pages with - the same alias, the HTML display of all the selections was not -- produced. (\PR{15282}) -- -+ produced. (\PR{15282}) -+ - \item \code{splinefun(method="monoH.FC")} now produces a - function with first argument named \code{x} and allows -- \code{deriv=3}, as documented. (\PR{15273}) -- -- \item \code{summaryRprof()} would only read the first -+ \code{deriv=3}, as documented. (\PR{15273}) -+ -+ \item \code{summaryRprof()} would only read the first - \code{chunksize} lines of an \code{Rprof} file produced with - \code{line.profiling=TRUE}. By default, this is the first 100 - seconds. (\PR{15288}) -- -+ - \item \code{lsfit()} produced an incorrect error message when - argument \code{x} had more columns than rows or \code{x} had a -- different number of rows than \code{y}. (Spotted by Renaud Gaujoux.) -+ different number of rows than \code{y}. (Spotted by Renaud Gaujoux.) - - \item Binary operations on equal length vectors copied the - class name from the second operand when the first had no -diff -ruN R-3.0.1/doc/html/NEWS.html R-patched/doc/html/NEWS.html ---- doc/html/NEWS.html 2013-05-16 03:05:47.000000000 -0400 -+++ doc/html/NEWS.html 2013-05-26 18:10:20.000000000 -0400 -@@ -8,6 +8,76 @@ - - <h2> R News</h2> - -+<h3><img src="../help/figures/../../html/logo.jpg" alt="../../html/logo.jpg" /> CHANGES IN R 3.0.1 patched</h3> -+ -+ -+ -+<h4>NEW FEATURES</h4> -+ -+ -+<ul> -+<li><p> The macros used for the texinfo manuals have been changed to -+work better with the incompatible changes made in texinfo 5.x. -+</p> -+</li> -+<li><p> The <code>example()</code> and <code>tools::Rd2ex()</code> functions now -+have parameters to allow them to ignore </p> -+<PRE>\dontrun</PRE> markup in -+examples. (Suggested by Peter Solymos.) -+</li></ul> -+ -+ -+ -+ -+<h4>C-LEVEL FACILITIES</h4> -+ -+ -+<ul> -+<li> <p>‘<span class="file">Rdefines.h</span>’ has been tweaked so it can be included in -+C++ code with ‘<span class="file">R_exts/Boolean.h</span>’ (which is included by -+‘<span class="file">R.h</span>’). Note though that ‘<span class="file">Rdefines.h</span>’ is not kept -+up-to-date, and ‘<span class="file">Rinternals.h</span>’ is preferred for new code. -+</p> -+</li></ul> -+ -+ -+ -+ -+<h4>BUG FIXES</h4> -+ -+ -+<ul> -+<li> <p><code>help.request()</code> could not determine the current version -+of <font face="Courier New,Courier" color="#666666"><b>R</b></font> on CRAN. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15241">PR#15241</a>) -+</p> -+</li> -+<li><p> On Windows, <code>file.info()</code> failed on root directories unless -+the path was terminated with an explicit <code>"."</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15302">PR#15302</a>) -+</p> -+</li> -+<li><p> The <code>regmatches<-()</code> replacement function mishandled -+results coming from <code>regexpr()</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15311">PR#15311</a>) -+</p> -+</li> -+<li><p> Documentation for <code>setClass</code> and -+<code>representation</code> still suggested the deprecated argument -+<code>representation=</code>. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15312">PR#15312</a>) -+</p> -+</li> -+<li> <p><CODE>R CMD config</CODE> failed in an installed build of <font face="Courier New,Courier" color="#666666"><b>R</b></font> -+3.0.1 (only) when a sub-architecture was used. (Reported by -+Berwin Turlach.) -+</p> -+</li> -+<li><p> On Windows, the installer modified the ‘<span class="file">etc/Rconsole</span>’ and -+‘<span class="file">etc/Rprofile.site</span>’ files even when default options were -+chosen. (Reported by Tal Galili.) -+</p> -+</li></ul> -+ -+ -+ -+ - <h3><img src="../help/figures/../../html/logo.jpg" alt="../../html/logo.jpg" /> CHANGES IN R 3.0.1</h3> - - -@@ -191,20 +261,20 @@ - <li><p> The return value when all workers failed from - <code>parallel::mclapply(mc.presechedule = TRUE)</code> was a list of - strings and not of error objects. (Spotted by Karl Forner and --Bernd Bischl.) -+Bernd Bischl.) - </p> - </li> - <li><p> In <font face="Courier New,Courier" color="#666666"><b>R</b></font> 3.0.0, when <code>help()</code> found multiple pages with - the same alias, the HTML display of all the selections was not --produced. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15282">PR#15282</a>) -+produced. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15282">PR#15282</a>) - </p> - </li> - <li> <p><code>splinefun(method="monoH.FC")</code> now produces a - function with first argument named <code>x</code> and allows --<code>deriv=3</code>, as documented. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15273">PR#15273</a>) -+<code>deriv=3</code>, as documented. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15273">PR#15273</a>) - </p> - </li> --<li> <p><code>summaryRprof()</code> would only read the first -+<li> <p><code>summaryRprof()</code> would only read the first - <code>chunksize</code> lines of an <code>Rprof</code> file produced with - <code>line.profiling=TRUE</code>. By default, this is the first 100 - seconds. (<a href="https://bugs.R-project.org/bugzilla3/show_bug.cgi?id=15288">PR#15288</a>) -@@ -212,7 +282,7 @@ - </li> - <li> <p><code>lsfit()</code> produced an incorrect error message when - argument <code>x</code> had more columns than rows or <code>x</code> had a --different number of rows than <code>y</code>. (Spotted by Renaud Gaujoux.) -+different number of rows than <code>y</code>. (Spotted by Renaud Gaujoux.) - </p> - </li> - <li><p> Binary operations on equal length vectors copied the -diff -ruN R-3.0.1/doc/html/R-admin.html R-patched/doc/html/R-admin.html ---- doc/html/R-admin.html 2013-05-16 03:11:03.000000000 -0400 -+++ doc/html/R-admin.html 2013-05-26 18:15:13.000000000 -0400 -@@ -245,7 +245,7 @@ - - <p>This is a guide to installation and administration for R. - -- <p>The current version of this document is 3.0.1 (2013-05-16). -+ <p>The current version of this document is 3.0.1 Patched (2013-05-26). - - <p> - -@@ -986,7 +986,7 @@ - perhaps for some network-mounted systems). - - <p>Installation is <em>via</em> the installer --<samp><span class="file">R-3.0.1-win.exe</span></samp>. Just double-click on the icon and -+<samp><span class="file">R-3.0.1patched-win.exe</span></samp>. Just double-click on the icon and - follow the instructions. When installing on a 64-bit version of Windows - the options will include 32- or 64-bit versions of R (and the default is - to install both). You can uninstall R from the Control Panel. -@@ -1286,7 +1286,7 @@ - installation (in double quotes if it contains spaces or backslashes). - - <p>Both methods create an executable with a standard name such as --<samp><span class="file">R-3.0.1-win.exe</span></samp>, so please rename it to indicate that -+<samp><span class="file">R-3.0.1patched-win.exe</span></samp>, so please rename it to indicate that - it is customized. If you intend to <em>distribute</em> a customized - installer please do check that license requirements are met – note that - the installer will state that the contents are distributed under GPL-2 -@@ -1338,21 +1338,21 @@ - make msi - </pre> - <p class="noindent">which will result in a file with a name like --<samp><span class="file">R-3.0.1-win32.msi</span></samp>. This can be double-clicked to be -+<samp><span class="file">R-3.0.1patched-win32.msi</span></samp>. This can be double-clicked to be - installed, but those who need it will know what to do with it (usually - by running <samp><span class="command">msiexec /i</span></samp> with additional options). Properties - that users might want to set from the <samp><span class="command">msiexec</span></samp> command line - include ‘<samp><span class="samp">ALLUSERS</span></samp>’, ‘<samp><span class="samp">INSTALLDIR</span></samp>’ (something like --<samp><span class="file">c:\Program Files\R\R-3.0.1</span></samp>) and ‘<samp><span class="samp">RMENU</span></samp>’ (the path -+<samp><span class="file">c:\Program Files\R\R-3.0.1patched</span></samp>) and ‘<samp><span class="samp">RMENU</span></samp>’ (the path - to the ‘<samp><span class="samp">R</span></samp>’ folder on the start menu) and ‘<samp><span class="samp">STARTDIR</span></samp>’ (the - starting directory for R shortcuts, defaulting to something like - <samp><span class="file">c:\Users\name\Documents\R</span></samp>). - - <p>The MSI installer can be built both from a 32-bit build of R --(<samp><span class="file">R-3.0.1-win32.msi</span></samp>) and from a 64-bit build of R --(<samp><span class="file">R-3.0.1-win64.msi</span></samp>, optionally including 32-bit files -+(<samp><span class="file">R-3.0.1patched-win32.msi</span></samp>) and from a 64-bit build of R -+(<samp><span class="file">R-3.0.1patched-win64.msi</span></samp>, optionally including 32-bit files - by setting the macro <code>HOME32</code>, when the name is --<samp><span class="file">R-3.0.1-win.msi</span></samp>). Unlike the main installer, a 64-bit -+<samp><span class="file">R-3.0.1patched-win.msi</span></samp>). Unlike the main installer, a 64-bit - MSI installer can only be run on 64-bit Windows. - - <p>Thanks to David del Campo (Dept of Statistics, University of Oxford) -@@ -1421,10 +1421,6 @@ - should run on all Macs from mid-2008 on. For older Intel Macs and some - older versions of the OS you can install R from the sources. - -- <p>Note that unlike <acronym>CRAN</acronym> binary distributions of R 2.x.y, --there is only a 64-bit version (and hence no separate <code>R64.app</code> --application, nor <samp><span class="command">R64</span></samp>/<samp><span class="command">R32</span></samp> front-ends). -- - <p>To install, just double-click on the icon of the file you downloaded. - At the `Installation Type' stage, note the option to `Customize'. This - currently shows three components (`Package Name'). Everyone will need -@@ -1789,8 +1785,7 @@ - <acronym>CRAN</acronym> or local files. - - <p>Note that many binary packages including compiled code are tied to a --particular series (e.g. R 2.15.x or 3.0.x) of R: in any case R 3.0.x --cannot use any binary packages built for R 2.15.x or earlier. -+particular series (e.g. R 3.0.x or 3.1.x) of R. - - <p>Installing source packages which do not contain compiled code should - work with no additional tools. For others you will need the `Command -@@ -2611,7 +2606,7 @@ - <samp><span class="file">texinfo.tex</span></samp> need to be compatible: we have seen problems with - older TeX distributions (TeXLive 2007 and MiKTeX 2.8) used with - <strong>texinfo</strong> 4.13. It should be possible to use <samp><span class="command">makeinfo</span></samp> --version 5.0, but e.g.. 4.13 produces better-formatted output. -+version 5.x. - - <p><a name="index-Vignettes-69"></a>The PDF documentation (including <samp><span class="file">doc/NEWS.pdf</span></samp>) and building - vignettes needs <samp><span class="command">pdftex</span></samp> and <samp><span class="command">pdflatex</span></samp>. We require -@@ -4693,7 +4688,7 @@ - - <h3 class="section">D.2 The Inno Setup installer</h3> - --<p>To make the installer package (<samp><span class="file">R-3.0.1-win.exe</span></samp>) we -+<p>To make the installer package (<samp><span class="file">R-3.0.1patched-win.exe</span></samp>) we - currently require the Unicode version of Inno Setup 5.3.7 or later from - <a href="http://jrsoftware.org/">http://jrsoftware.org/</a>. This is <em>not</em> included in - <samp><span class="file">Rtools*.exe</span></samp>. -diff -ruN R-3.0.1/doc/manual/R-admin.texi R-patched/doc/manual/R-admin.texi ---- doc/manual/R-admin.texi 2013-04-29 07:05:23.000000000 -0400 -+++ doc/manual/R-admin.texi 2013-05-24 18:05:06.000000000 -0400 -@@ -1473,10 +1473,6 @@ - should run on all Macs from mid-2008 on. For older Intel Macs and some - older versions of the OS you can install @R{} from the sources. - --Note that unlike @acronym{CRAN} binary distributions of @R{} 2.x.y, --there is only a 64-bit version (and hence no separate @code{R64.app} --application, nor @command{R64}/@command{R32} front-ends). -- - To install, just double-click on the icon of the file you downloaded. - At the `Installation Type' stage, note the option to `Customize'. This - currently shows three components (`Package Name'). Everyone will need -@@ -1904,8 +1900,7 @@ - @acronym{CRAN} or local files. - - Note that many binary packages including compiled code are tied to a --particular series (e.g.@: @R{} 2.15.x or 3.0.x) of @R{}: in any case @R{} 3.0.x --cannot use any binary packages built for @R{} 2.15.x or earlier. -+particular series (e.g.@: @R{} 3.0.x or 3.1.x) of @R{}. - - Installing source packages which do not contain compiled code should - work with no additional tools. For others you will need the `Command -@@ -2863,7 +2858,7 @@ - @file{texinfo.tex} need to be compatible: we have seen problems with - older @TeX{} distributions (TeXLive 2007 and MiKTeX 2.8) used with - @pkg{texinfo} 4.13. It should be possible to use @command{makeinfo} --version 5.0, but e.g..@: 4.13 produces better-formatted output. -+version 5.x. - - @cindex Vignettes - The PDF documentation (including @file{doc/NEWS.pdf}) and building -diff -ruN R-3.0.1/doc/manual/R-defs.texi R-patched/doc/manual/R-defs.texi ---- doc/manual/R-defs.texi 2013-04-03 18:05:07.000000000 -0400 -+++ doc/manual/R-defs.texi 2013-05-24 18:05:06.000000000 -0400 -@@ -17,16 +17,18 @@ - @acronym{HTML} - @end macro - --@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) - |