Commit 83ac0cb7 authored by Dirk Eddelbuettel's avatar Dirk Eddelbuettel

Import Upstream version 2.10.1

parent 29acb93a

* *
* 2.10 SERIES NEWS *
......@@ -6,6 +6,191 @@
o The PCRE library has been updated to version 8.00.
o R CMD INSTALL has new options --no-R, --no-libs, --no-data,
--no-help, --no-demo, --no-exec, and --no-inst to suppress
installation of the specified part of the package. These are
intended for special purposes (e.g. building a database
of help pages without fully installing all packages).
o The documented line-length limit of 4095 bytes when reading
from the console now also applies also to parse(file="")
(which previously had a limit of around 1024 bytes).
o A Bioconductor mirror can be set for use by setRepositories()
via the option "BioC_mirror", e.g. the European mirror can be
selected by
o Double-clicking in a tk_select.list() list box now selects the
item and closes the list box (as happens on the Windows
select.list() widget).
o configure will be able to find a usable libtiff in some rare
circumstances where it did not previously (where libtiff
needed to be linked explicitly against -ljpeg).
o Making refman.pdf works around a problem with the indexing
with hyperref 6.79d and later.
o The 'extended' argument is deprecated in strsplit(), grep(),
grepl(), sub(), gsub(), regexpr() and gregexpr() (not just the
value extended = FALSE) and will be removed in R 2.11.0.
o trigamma(x) and other psigamma(x, n) calls are now accurate for
very large abs(x). (PR#14020)
o [g]sub(perl=FALSE, fixed=FALSE) could use excessive stack space
when used with a very long vector containing some non-ASCII
o The default method of weighted.mean(na.rm = TRUE) did not omit
weights for NA observations in 2.10.0. (PR#14032)
o [g]regexpr(pattern, fixed = TRUE) returned match positions in
bytes (not characters) in an MBCS locale if 'pattern' was a
single byte.
[g]sub(fixed = TRUE) with a single-byte pattern could
conceivably have matched part of a multibyte character in a
non-UTF-8 MBCS.
o findLineNum() and setBreakpoint() would sometimes fail if the
specified file was not in the current directory.
o Package tcltk's demo(tkdensity) was broken in 2.9.0 when demo()
was changed to set par(ask = TRUE).
o gsub() with backrefs could fail on extremely long strings
(hundreds of thousands of characters) due to integer overflow
in a length calculation.
o abline(*, untf=TRUE) now uses a better x-grid in log-scale, e.g.,
for plot(c(1,300), c(1,300), log="xy") ; abline(4,1, untf=TRUE).
o detach/unloadNamespace() arrange to flush the package's
lazyload cache of R objects once the package/namespace is no
longer needed.
o There have been small fixes to the rendering of help,
e.g. \command is now rendered verbatim (so e.g. -- is not
interpreted, PR#14045).
Also, there are many small changes to help files where the new
converters were not rendering them in the same way as before.
o available.packages() would fail when run on a repository
with no packages meeting the filtering conditions. (PR#14042)
o rep(x, times, each = 2) gave invalid results when the 'times'
argument is a vector longer than 'x'. Reported by Bill Dunlap.
o An error when unloadNamespace() attempted to run the .onUnload()
function gave an error in the reporting function and so was
not reported properly.
o Text help rendering did not handle very long input lines
o promptMethods() generated signature documentation improperly.
o pgamma(x, a, lower.tail=FALSE) and qgamma(..) are now
considerably more accurate in some regions for very small 'a'.
qgamma() now correctly returns 0 instead of NaN in similar
extreme cases, and qgamma() no longer warns in the case of
small 'a', see (PR#12324).
o unname() now also removes names from a zero length vector.
o Printing results from ls.str() no longer evaluates unevaluated
o complete.cases() failed on a 0-column data frame argument.
(Underlies PR#14066.)
It could return nonsensical results if no input determined the
number of cases (seen in the no-segfault tests).
o An error in nls() with a long formula could cause a segfault.
o qchisq(p, df, ncp, lower.tail = FALSE) with ncp >= 80 was
inaccurate for small p (as the help page said): it is now
less inaccurate. (In part, PR#13999.)
For ncp less than but close to 80, pchisq() and qchisq() are
more accurate for probablilities very close to 1 (a series
expansion was truncated slightly too early).
pchisq(x, df, ncp) can no longer return values just larger
than one for large values of ncp.
o intToUtf8() could fail when asked to produce 10Mb or more
strings, something it was never intended to do: unfortunately
Windows crashed R (other OSes reported a lack of resources).
o chisq.test() could fail when given argument 'x' or 'y' which
deparsed to more than one line. (Reported by Laurent Gauthier.)
o S4 methods are uncached whenever the name space containing
them is unloaded (by unloadNamespace() as well as by
detach(unload = TRUE)).
o The internal record-keeping by dyn.load/dyn.unload was
incomplete, which could crash R if a DLL that registered
.External routines had earlier been unloaded.
o bessel[JY](x, nu) with nu a negative integer (a singular case)
is now correct, analogously to besselI(), see PR#13556, below.
o tools::file_path_as_absolute() doubled the file separator when
applied to a file such as "/vmunix" or (on Windows) "d:/afile"
in a directory for which getwd() would return a path with a
trailing separator (largely cosmetic, as reasonable file
systems handle such a path correctly). (Perhaps what was
meant by PR#14078.)
o unsplit(drop = TRUE) applied to a data frame failed to pass
'drop' to the computation of row names. (PR#14084)
o The "difftime" method of mean() ignored its 'na.rm' argument.
o tcltk::tk_select.list() is now more likely to remove the
widget immediately after selection is complete.
o Adding/subtracting a "difftime" object to/from a "POSIXt" or
"Date" object works again (it was broken by the addition of
o Conversion to latex of an Rd file with no aliases failed.
o wilcox.test(*, has achieved.level corrected and, for
exact=FALSE, now gives an 'estimate' which does not depend on the
alternative used.
o failed when the package argument was specified.
o switch(EXPR = "A") now returns NULL, as switch(1) {which used to
signal an error}.
......@@ -245,7 +430,7 @@ NEW FEATURES
always stored in UTF-8 (and hence is suitable for portably
including Unicode text in packages).
o New as.raw() method for "tclObj" objects (wish of PR#13578).
o New as.raw() method for "tclObj" objects (wish of PR#13758).
o Rd.sty now makes a better job of setting email addresses,
including using a monospaced font.
......@@ -397,7 +582,7 @@ HELP & Rd FILE CHANGES
controlled using tools::startDynamicHelp(). With this enabled,
HTML help pages will be generated on request, resolving links
by searching through the current .libPaths(). The user
may set option("help.ports") to control which IP port is used
may set options("help.ports") to control which IP port is used
by the server.
o help.start() no longer sets options(htmlhelp = TRUE) (it used
Revision: 50208
Last Changed Date: 2009-10-26
Revision: 50720
Last Changed Date: 2009-12-14
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.61 for R 2.10.0.
# Generated by GNU Autoconf 2.61 for R 2.10.1.
# Report bugs to <>.
......@@ -723,8 +723,8 @@ SHELL=${CONFIG_SHELL-/bin/sh}
# Identity of this package.
......@@ -1663,7 +1663,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
\`configure' configures R 2.10.0 to adapt to many kinds of systems.
\`configure' configures R 2.10.1 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
......@@ -1738,7 +1738,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
short | recursive ) echo "Configuration of R 2.10.0:";;
short | recursive ) echo "Configuration of R 2.10.1:";;
cat <<\_ACEOF
......@@ -1946,7 +1946,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
R configure 2.10.0
R configure 2.10.1
generated by GNU Autoconf 2.61
Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
......@@ -1960,7 +1960,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by R $as_me 2.10.0, which was
It was created by R $as_me 2.10.1, which was
generated by GNU Autoconf 2.61. Invocation command line was
$ $0 $@
......@@ -45639,13 +45639,14 @@ fi
# may need to resolve jpeg routines
{ echo "$as_me:$LINENO: checking for TIFFOpen in -ltiff" >&5
echo $ECHO_N "checking for TIFFOpen in -ltiff... $ECHO_C" >&6; }
if test "${ac_cv_lib_tiff_TIFFOpen+set}" = set; then
echo $ECHO_N "(cached) $ECHO_C" >&6
LIBS="-ltiff $LIBS"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
......@@ -48428,11 +48429,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
(eval echo "\"\$as_me:48431: $lt_compile\"" >&5)
(eval echo "\"\$as_me:48432: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
cat conftest.err >&5
echo "$as_me:48435: \$? = $ac_status" >&5
echo "$as_me:48436: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
......@@ -48527,11 +48528,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
(eval echo "\"\$as_me:48530: $lt_compile\"" >&5)
(eval echo "\"\$as_me:48531: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
cat out/conftest.err >&5
echo "$as_me:48534: \$? = $ac_status" >&5
echo "$as_me:48535: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
# The compiler can only warn and ignore the option if not recognized
......@@ -48579,11 +48580,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
(eval echo "\"\$as_me:48582: $lt_compile\"" >&5)
(eval echo "\"\$as_me:48583: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
cat out/conftest.err >&5
echo "$as_me:48586: \$? = $ac_status" >&5
echo "$as_me:48587: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
# The compiler can only warn and ignore the option if not recognized
......@@ -59273,7 +59274,7 @@ exec 6>&1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
This file was extended by R $as_me 2.10.0, which was
This file was extended by R $as_me 2.10.1, which was
generated by GNU Autoconf 2.61. Invocation command line was
......@@ -59326,7 +59327,7 @@ Report bugs to <>."
R config.status 2.10.0
R config.status 2.10.1
configured by $0, generated by GNU Autoconf 2.61,
with options \\"`echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
......@@ -2045,7 +2045,8 @@ R_PCRE
## libtiff
AC_CHECK_LIB(tiff, TIFFOpen, [have_tiff=yes], [have_tiff=no], [])
# may need to resolve jpeg routines
AC_CHECK_LIB(tiff, TIFFOpen, [have_tiff=yes], [have_tiff=no], [${BITMAP_LIBS}])
if test "x${ac_cv_header_tiffio_h}" = xyes ; then
if test "x${have_tiff}" = xyes; then
AC_DEFINE(HAVE_TIFF, 1, [Define this if libtiff is available.])
Frequently Asked Questions on R
Version 2.10.2009-10-23
Version 2.10.2009-12-10
ISBN 3-900051-08-9
Kurt Hornik
......@@ -255,7 +255,7 @@ sparc-sun-solaris.
2.3 What is the current version of R?
The current released version is 2.10.0. Based on this
The current released version is 2.10.1. Based on this
`major.minor.patchlevel' numbering scheme, there are two development
versions of R, a patched version of the current release (`r-patched') and
one working towards the next minor or eventually major (`r-devel') releases
......@@ -17,6 +17,7 @@ Claus Ekstrom <>
Sebastian Fischmeister <>
John Fox <>
Paul Gilbert <>
Gabor Grothendieck <>
Frank E Harrell Jr <>
Torsten Hothorn <>
Robert King <>
......@@ -213,7 +213,7 @@ span.env{font-family: monospace}
<p>This is a guide to installation and administration for R.
<p>The current version of this document is 2.10.0 (2009-10-26).
<p>The current version of this document is 2.10.1 (2009-12-14).
<p>ISBN 3-900051-09-7
......@@ -624,7 +624,7 @@ specified on the <samp><span class="command">make install</span></samp> command
<code>libdir</code>. The C header files can be installed to the value of
<code>rincludedir</code>: note that as the headers are not installed into a
subdirectory you probably want something like
<p>If you want the R home to be something other than
<samp><var>libdir</var><span class="file">/R</span></samp>, use <samp><span class="option">rhome</span></samp>: for example
......@@ -855,7 +855,7 @@ from <acronym>CRAN</acronym> to run on Windows 2000 or later on ix86
<p>Your file system must allow long file names (as is likely except
perhaps for some network-mounted systems).
<p>Installation is <em>via</em> the installer <samp><span class="file">R-2.10.0-win32.exe</span></samp>.
<p>Installation is <em>via</em> the installer <samp><span class="file">R-2.10.1-win32.exe</span></samp>.
Just double-click on the icon and follow the instructions. You can
uninstall R from the Control Panel or from the (optional) R
program group on the Start Menu.
......@@ -893,11 +893,11 @@ will call this directory <var>R_HOME</var> below.
<p>You need to collect the following sets of files:
<li>Get the R source code <samp><span class="file">R-2.10.0.tar.gz</span></samp> from
<li>Get the R source code <samp><span class="file">R-2.10.1.tar.gz</span></samp> from
<acronym>CRAN</acronym>. Open a command window (or another shell) at
directory <var>R_HOME</var>, and run
<pre class="example"> tar xf R-2.10.0.tar.gz
<pre class="example"> tar xf R-2.10.1.tar.gz
<p class="noindent">to create the source tree in <var>R_HOME</var>. <strong>Beware</strong>: do use
<samp><span class="command">tar</span></samp> to extract the sources rather than tools such as WinZip
......@@ -1126,7 +1126,7 @@ customizations to that installation. Then in
installation (forward slashes and no spaces, please).
<p>Both methods create an executable with the standard name,
<samp><span class="file">R-2.10.0-win32.exe</span></samp>, so please rename it to indicate that
<samp><span class="file">R-2.10.1-win32.exe</span></samp>, so please rename it to indicate that
it is customized. If you intend to <em>distribute</em> a customized
installer please do check that license requirements are met &ndash; note that
the installer will state that the contents are distributed under GPL-2
......@@ -1168,7 +1168,7 @@ required. Then
make msi
<p class="noindent">which will results in a file of about 45Mb with a name like
<samp><span class="file">R-2.10.0-win32.msi</span></samp>. This can be double-clicked to be
<samp><span class="file">R-2.10.1-win32.msi</span></samp>. This can be double-clicked to be
installed, but those who need it will know what to do with it.
<p>Thanks to David del Campo (Dept of Statistics, University of Oxford)
......@@ -1218,7 +1218,7 @@ binaries for Mac OS X for a base distribution and a large number of
add-on packages from <acronym>CRAN</acronym> to run on Mac OS X version 10.4.4 or
<p>The simplest way is to use <samp><span class="file">R-2.10.0.dmg</span></samp>. Just
<p>The simplest way is to use <samp><span class="file">R-2.10.1.dmg</span></samp>. Just
double-click on the icon and the disk image file will be mounted. Read
the <samp><span class="file">ReadMe.txt</span></samp> inside the disk image and follow the instructions.
......@@ -1233,8 +1233,8 @@ mentioned <a href="">R for
and install some tools as explained in the document. Then you have to
expand the R sources and configure R appropriately, for example
<pre class="example"> tar zxvf R-2.10.0.tar.gz
cd R-2.10.0
<pre class="example"> tar zxvf R-2.10.1.tar.gz
cd R-2.10.1
./configure --with-blas='-framework vecLib' --with-lapack \
--with-aqua --enable-R-framework
......@@ -2097,7 +2097,10 @@ and <samp><span class="command">latex</span></samp>, or <samp><span class="comma
<p>If you want to build from the R Subversion repository you need both
<samp><span class="command">makeinfo</span></samp> and <samp><span class="command">pdflatex</span></samp>.
<a name="index-Subversion-67"></a>
<a name="Useful-libraries-and-programs"></a>
The essential programs should be in your <samp><span class="env">PATH</span></samp> at the time
<samp><span class="command">configure</span></samp> is run: this will capture the full paths.
<p><a name="Useful-libraries-and-programs"></a>
<h3 class="section">A.2 Useful libraries and programs</h3>
......@@ -2138,10 +2141,6 @@ rather similar to the first two
later) and <code>zlib</code> (version 1.1.3 or later) or <code>libtiff</code> (any
recent version &ndash; 3.8.2 was tested) respectively.
<p>The <code>bitmap</code> and <code>dev2bitmap</code> devices and also
<code>embedFonts()</code> use ghostscript
(<a href=""></a>).
<p>If you have them installed (including the appropriate headers and of
recent enough versions), <code>zlib</code>, <code>libbz2</code> and PCRE will be
used if specified by <samp><span class="option">--with-system-zlib</span></samp>,
......@@ -2172,15 +2171,22 @@ Linux distributions, Solaris 9/10, AIX and Windows, usually as
available (including on Mac OS X &gt;= 10.4).
<p>Code developers will need Perl version 5.8.0 or later, available via
<a href=""></a>. This is use to package and check
<a href=""></a>. This is used to package and check
packages, for <samp><span class="command">R CMD Rprof</span></samp><a rel="footnote" href="#fn-19" name="fnd-19"><sup>19</sup></a> and the rarely used <samp><span class="command">R
CMD Sd2Rd</span></samp>.
CMD Sd2Rd</span></samp>: it should be in your <samp><span class="env">PATH</span></samp> when <samp><span class="command">configure</span></samp> is
<!-- The Perl scripts left are -->
<!-- src/scripts: Rprof Sd2Rd build check -->
<!-- tools: -->
<!-- src/gnuwin32/fixed/ -->
<!-- src/gnuwin32/installer: -->
<p>The <code>bitmap</code> and <code>dev2bitmap</code> devices and also
<code>embedFonts()</code> use ghostscript
(<a href=""></a>). This should either be in your
path when the command is run, or its full path specified by the
environment variable <samp><span class="env">R_GSCMD</span></samp> at that time.
<p><a name="Tcl%2fTk"></a>
<a name="Tcl_002fTk"></a>
......@@ -2696,7 +2702,7 @@ produce the default.)
should take a value of an executable in the user's path or specify
a full path.
<p><a name="index-R_005fPDFVIEWER-81"></a>Its counterpart for PDF file is <samp><span class="env">R_PDFVIEWER</span></samp>.
<p><a name="index-R_005fPDFVIEWER-81"></a>Its counterpart for PDF files is <samp><span class="env">R_PDFVIEWER</span></samp>.
<p><a name="Compilation-flags"></a>
......@@ -3672,7 +3678,7 @@ Perl is essential to build R, and needed to develop packages.
<p>A complete build of R including compiled <acronym>HTML</acronym> help files and
PDF manuals, and producing the standalone installer
<samp><span class="file">R-2.10.0-win32.exe</span></samp> will also need the following:
<samp><span class="file">R-2.10.1-win32.exe</span></samp> will also need the following:
<li>The Inno Setup installer
......@@ -3745,7 +3751,7 @@ suitably; ensure you have the required fonts installed.