Commit f4b31cf7 authored by Dirk Eddelbuettel's avatar Dirk Eddelbuettel

Import Upstream version 2.7.2

parent afc4307d
......@@ -99,7 +99,7 @@ svnonly:
@if test ! -f "$(srcdir)/doc/FAQ" || test -f non-tarball ; then \
(cd doc/manual && $(MAKE) front-matter html-non-svn) ; \
touch non-tarball ; \
(cd $(srcdir); LC_ALL=C TZ=GMT svn -rHEAD info || $(ECHO) "Revision: unknown") 2> /dev/null \
(cd $(srcdir); LC_ALL=C TZ=GMT svn info || $(ECHO) "Revision: unknown") 2> /dev/null \
| sed -n -e '/^Revision/p' -e '/^Last Changed Date/'p \
| cut -d' ' -f1,2,3,4 > SVN-REVISION-tmp ; \
$(top_srcdir)/tools/move-if-change SVN-REVISION-tmp SVN-REVISION ; \
......
......@@ -6,6 +6,173 @@
**************************************************
CHANGES IN R VERSION 2.7.2
NEW FEATURES
o sprintf() returns elements of the result in UTF-8 when the
format or any character input has a corresponding element
declared as UTF-8. Similarly for paste(), elements of the
result are in UTF-8 when any input to that element is declared
as UTF-8.
o axis() has new arguments 'col.ticks' and 'lwd.ticks' to allow
the colour and line width of ticks to be set separately from
that of the line (e.g. to set one or the other to transparent
or zero width).
o legend() has a new argument 'box.col' to set the colour of the
enclosing box.
o legend() gains a 'xpd' argument to make it easier to place a
legend in the margins or outer margins.
o stripchart() now passes '...' to title() (as well as to
plot.default() and axis()). (Wish of PR#12202)
o help.search() has new argument 'searchEngine' to go
directly to the search form: this is needed by users of
Firefox 3 to workaround a bug in interpreting the search
results pages.
BUG FIXES
o Plotmath computed the glyph metrics for the wrong character (and
perhaps for a non-existent one) if this was a single-byte
character with the top bit set. An example was symbol("\300").
o sink() and cat() could divert output to a non-writable connection.
o phyper(x, 0,0,0) no longer hangs for huge x and gives 1 for x >= 0.
(PR#11813)
o plnorm(x, ..., log.p=TRUE) is now correct for x <= 0. (PR#11867)
o <data.frame>[, ch] gives an error (again!) when ch is a string not
exactly matching the column names, thanks to an oral bug report by
Matthew Dowle.
o data.frame(x=1:2, y=3:4, row.names=c("a","NA"))[c(2,NA),] has
correct row names c("NA,"NA.1") again.
o The GUI data editor for dataframes did not handle escape
characters in entries properly. (PR#11897)
o PCRE has been updated to 7.7 (bugfix release).
o package.skeleton() wrongly warned about invalid code_files names
when these were not in the current directory.
o shapiro.test(c(0,0,1)) now has P value >= 0 (instead of barely
negative).
o assign() now warns if given a character vector of length > 1,
rather than silently taking the first element.
o rcond(<exactly singular matrix>) now gives 0 instead of an error.
o There was a memory leak in C function ucstoutf8 used by some
graphics devices.
o Plots of profile.mle() objects (package 'stats4') were
misbehaving when the 'which' argument had been used in their
calculation.
o dnbinom(x, size, mu=*, ..) is now more accurate for very large
'size'. The same applies to pnbinom() and rnbinom().
o axis() was ignoring par() mgp[3] if mgp was set in-line.
o Closing an X11 View() or dataentry window via its frame's
close control now works better on some window managers.
o Calling lapply() was not handling method dispatch correctly for
is.numeric(), is.matrix(), is.array(), log() and the Math2
group. This affected data.matrix() which incorrectly regarded
"Date" and "POSIXct" objects as numeric, and has been adjusted
to do so as exceptions.
o package.skeleton() was not looking for non-function objects in
its 'environment' argument.
o nls() was only finding its 'weights' argument in the case when
all the variables in the formula were of the same length and
hence that model.frame() could be used.
It was silently ignoring 'subset' and 'na.action' except in
that case. Now they are ignored only if 'data' is a list and
variables taken from 'data' are not all of the same length,
in which case a warning is given.
o The 'mle' confint() method now takes 'level' into account when
setting 'alpha' for the profile.
o within() was not handling correctly expressions that produced
NULL columns. (PR#11131)
o dev.print() and dev.copy2{eps,pdf}() now ensure that the current
device is restored as the active device even if an error
occurs. (PR#9801)
o as.Date() could fail to convert character strings representing
days on which midnight did not exist in the current timezone
(as happened in parts of Africa on 1960-01-01).
o The automatic placement of legend() with 'title' and a
reversed 'x' axis was incorrect. (PR#12019)
o The use of multiple packages in 'LinkingTo' works again, and
now works when the dependent packages are in the library to be
installed to (but not in the library path seen by R --vanilla).
o bxp() (and hence boxplot) now respects in-line graphical
parameters 'xaxp'/'yaxp' as appropriate. (PR#11463)
o barplot(log = "y") failed if there were NAs in the 'height'
argument. (PR#11585)
o pbeta() is more accurate in some cases with extreme values of
'ncp'. (PR#11277).
o edit.data.frame() no longer fails if called on a 0-column
data frame and no column is created.
o pchisq(x, df=0) was always one even for x < 0; similarly for
pgamma(x, alpha=0).
o add1() and drop1() now return a P-value of NaN in cases with
df=0 for test="Chisq" (they gave NaN until pchisq was altered
in R 2.6.2).
o The default methods of drop1() and add1() now re-evaluate in the
object's formula environment, rather than simply in the parent
(informal bug report by Werner Stahel).
o The undocumented limit of 8191 bytes on comments (from # to
the end of the line) in R code has been removed.
o qgamma() warns if used with shape < 1e-10, when it may be
unreliable. (PR#12324)
o Installing a source package was not using the package's declared
encoding (if any) as a default encoding for the help.search()
database in Meta/hsearch.rds. This could cause packages with
a default encoding to have some of their entries rejected by
help.search() in a multi-byte locale (such as a UTF-8 locale).
o duplicated() and unique() now handle 'incomparables' better,
and avoid occasional segfaults (PR#12551).
o data.frame(row.names=NULL) once again behaves differently from
the default (as documented).
o plot(isoreg(x,y)) now plots the points correctly, also when 'x'
is not sorted.
CHANGES IN R VERSION 2.7.1
......@@ -842,6 +1009,9 @@ BUG FIXES
(Note that this is pretty arbitrary, but zero-length vectors
always give an error so it is at least consistent.)
Since sd(na.rm=TRUE) and var(na.rm=TRUE) both call cov(use =
"complete.obs"), this applies also to them.
cor(use="pair") used to give diagonal 1 even if the variable
was completely missing for the rank methods but NA for the
Pearson method: it now gives NA in all cases.
......
Revision: 45970
Last Changed Date: 2008-06-23
Revision: 46428
Last Changed Date: 2008-08-25
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......@@ -50,6 +50,11 @@ function searchInIndex (searchTerm, searchDesc,
<h1>Search Engine <img class=toplogo src="../logo.jpg"></h1>
<div align="center">
<a href="../index.html"><img src="../up.jpg"
alt="[Top]" width="30" height="30" border="0"></a>
</div>
<hr width="100%">
<h2>Search</h2>
......
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......@@ -996,7 +996,7 @@ You can test a build by running @code{make check}. You may need to set
@enindex TMPDIR
@env{TMPDIR} to the absolute path to a suitable temporary directory: the
default is @samp{c:/TEMP}. (Use forward slashes and do not use a path
including spaces.)
including spaces. It will be ignored if not set to a directory.)
The recommended packages can be checked by
......@@ -1135,12 +1135,14 @@ It is also possible to build an installer for use with Microsoft
Installer. This is intended for use by sysadmins doing automated
installs, and is not recommended for casual use.
It makes use of the Windows Installer XML (WiX) toolkit available from
@uref{http://wix.sourceforge.net/}: we tested version 2.0. (This needs
the .NET 1.1 framework installed: it ran on a vanilla Windows XP SP2
machine. Probably Windows 2000 or later is required by some of the
features used.) Once WiX is installed, set the path to its home
directory in @file{MkRules}.
It makes use of the Windows Installer XML (WiX) toolkit (wersion 2.0)
available from @uref{http://wix.sourceforge.net/}. (This needs the .NET
1.1 framework installed: it ran on a vanilla Windows XP SP2
machine. Unfortunately the file format has been changed within the same
version: currently our code works with releases 2.0.4221.0 and
2.0.5805.0 -- the latter is now said to be `production/stable' so
hopefully there will be no more format changes.) Once WiX is installed,
set the path to its home directory in @file{MkRules}.
You need to have the files for a complete R build, including bitmap and
Tcl/Tk support and the manuals, as well as the recommended packages.
......@@ -1175,8 +1177,12 @@ You will need suitable cross-compilers installed and in your path. We
do not at present distribute suitable cross-compilers.
For Fedora 8 and 9 users, RPMs are available at
@uref{http://sourceforge.net/projects/mingw-cross/}, currently of
@command{gcc} 4.3.0 for both @cputype{ix86} and @cputype{x86_64}.
@uref{http://sourceforge.net/projects/@/mingw-cross/} for both
@cputype{ix86} and @cputype{x86_64}. (Currently there are Fedora 8 RPMs
for 4.3.0 and Fedora 9 RPMs for both 4.3.0 and 4.3.1. The Fedora 8
@cputype{x86_64} RPMs have been tested.) Recent Debian and Ubuntu
versions have C/C++ (but it seems not Fortran) cross-compilers based on
@command{gcc} 4.2.1.
@c There is currently a complete set of tools based on @command{gcc} 3.4.5
@c at @uref{http://www.stats.ox.ac.uk/pub/Rtools/i586-cross-tools.tar.bz2,
......@@ -4234,7 +4240,21 @@ be invoked as @command{xlf_r}.
The AIX native @code{iconv} does not support encodings @samp{latin1} nor
@samp{""} and so cannot be used. (As far as we know GNU @code{libiconv}
could be installed.)
could be installed.) Fan Long reports success on AIX 5.3 using
@c https://stat.ethz.ch/pipermail/r-devel/2008-August/050318.html
@example
OBJECT_MODE=64
LIBICONV=/where/libiconv/installed
CC="xlc_r -q64"
CFLAGS="-O -qstrict"
CXX="xlC_r -q64"
CXXFLAGS="-O -qstrict"
F77="xlf_r -q64"
AR="ar -X64"
CPPFLAGS="-I$LIBICONV/include -I/usr/lpp/X11/include/X11"
LDFLAGS="-L$LIBICONV/lib -L/usr/lib -L/usr/X11R6/lib"
@end example
@node Cygwin, New platforms, AIX, Platform notes
@section Cygwin
......@@ -4362,6 +4382,14 @@ On Mozilla-based browsers the links on the results page will
become inactive if you return to it: to work around this you can open
a link in a new tab or window.
@c https://stat.ethz.ch/pipermail/r-help/2008-July/169521.html
There is a known issue with Firefox 3 (and 3.0.1). The links in the
results page may point to the wrong directory level. This is a bug in
the way Firefox is interpreting relative URLs, and can be circumvented
by opening the HTML search page (@file{.../doc/html/SearchEngine.html})
directly rather than from @file{.../doc/html/index.html} as shown by
@code{help.start()}.
Many thanks to Marc Schwartz in tracking down many of these issues with
enabling the Java search engine.
......@@ -4385,17 +4413,25 @@ Note that there appears not to be a Sun Java plugin for 64-bit browsers
on @cputype{x86_64} Linux:
(@uref{http://forum.java.sun.com/thread.jspa?threadID=568127&tstart=75,
@code{forum.java.sun.com/thread.jspa?threadID=568127&tstart=75}})
(although one is promised for Java 7) but 32-bit browsers have been used
on that platform.
Marc Schwartz reports that the `IcedTea' JVM that ships with Fedora 8
does not work with the search applet. On @cputype{ix86} the Sun JRE and
plugin can be instaled: see
(although one is expected for Java 6 in early 2009) but 32-bit browsers
have been used on that platform.
Marc Schwartz reports that the `IcedTea' (later called `OpenJDK') JVM
that ships with Fedora 8 and 9 does not work with the search applet.
(The bug report is part of
@uref{https://bugzilla.redhat.com/show_bug.cgi?id=304021,
@code{bugzilla.redhat.com/show_bug.cgi?id=304021}}.) On @cputype{ix86}
the Sun JRE and plugin can be installed: see
@uref{http://www.fedorafaq.org/#java, @code{www.fedorafaq.org/#java}}.
(The same FAQ documents the use of 32-bit Firefox on @cputype{x86_64}.)
(The same FAQ documents the use of 32-bit Firefox on @cputype{x86_64}.
See also
@uref{http://www.mjmwired.net/resources/mjm-fedora-f8.html#java,
@code{www.mjmwired.net/resources/mjm-fedora-f8.html#java}} and
@uref{http://www.mjmwired.net/resources/mjm-fedora-f9.html#java,
@code{www.mjmwired.net/resources/mjm-fedora-f9.html#java}}.)
Other Java installations, for example those from Blackdown and IBM, have
been used.
been used in the (not recent) past.
Older but still useful links are for Firefox/Mozilla,
@uref{http://plugindoc.mozdev.org/faqs/java.html,
......@@ -4434,7 +4470,9 @@ in Windows XP (SP1 or later), and which JVM is used by browser plugins
may also be controlled by the Sun Java applet in the Control Panel.
Recent versions of Internet Explorer may block the use of Java applets
and need the block removed @emph{via} the @emph{information bar}.
and need the block removed @emph{via} the @emph{information bar}. Also,
we have seen cases in which the search results come up as a blank page:
go back one page in the browser history to find the real results page.
Apple's Safari 3.0.4 also works.
......
......@@ -885,8 +885,10 @@ and return a list of data frames. If SAS is available on your system,
function @code{read.ssd} can be used to create and run a SAS script that
saves a SAS permanent dataset (@file{.ssd} or @file{.sas7bdat}) in
Transport format. It then calls @code{read.xport} to read the resulting
file. Package @pkg{Hmisc} has a similar function @code{sas.get}, also
running SAS.
file. (Package @pkg{Hmisc} has a similar function @code{sas.get}, also
running SAS.) For those without access to SAS but running on Windows,
the SAS System Viewer (a zero-cost download) can be used to open SAS
datasets and export them to e.g.@: @file{.csv} format.
@cindex S-PLUS
@findex read.S
......@@ -901,7 +903,7 @@ containing those.
Function @code{data.restore} reads S-PLUS data dumps (created by
@code{data.dump}) with the same restrictions (except that dumps from the
Alpha platform can also be read). It should be possible to read data
dumps from S-PLUS 5.x and 6.x written with @code{data.dump(oldStyle=T)}.
dumps from S-PLUS 5.x and later written with @code{data.dump(oldStyle=T)}.
If you have access to S-PLUS, it is usually more reliable to @code{dump}
the object(s) in S-PLUS and @code{source} the dumpfile in @R{}. For
......
......@@ -1464,7 +1464,9 @@ you will need to set it in the environment.
@code{R CMD check} and @code{R CMD build} need you to have installed the
files for building source packages (which is the default), as well as
the Windows toolset (see the ``R Installation and Administration''
manual).
manual). You may need to set @env{TMPDIR} to point to a suitable
writeable directory with a path not containing spaces -- use forward
slashes for the separators.
@end quotation
@node Customizing checking and building, , Building packages, Checking and building packages
......
......@@ -5108,7 +5108,7 @@ Here is an example from Bates & Watts (1988), page 51. The data are:
> y <- c(76, 47, 97, 107, 123, 139, 159, 152, 191, 201, 207, 200)
@end example
The model to be fitted is:
The fit criterion to be minimized is:
@example
> fn <- function(p) sum((y - (p[1] * x)/(p[2] + x))^2)
......@@ -7078,7 +7078,15 @@ You need to ensure that either the environment variables @env{TMPDIR},
valid place to create temporary files and directories.
Environment variables can be supplied as @samp{@var{name}=@var{value}}
pairs at the end of the command line.
pairs on the command line.
If there is an argument ending @file{.RData} (in any case) it is
interpreted as the path to the workspace to be restored: it implies
@option{--restore} and sets the working directory to the parent of the
named file. (This mechanism is used for drag-and-drop and file
association with @code{RGui.exe}, but also works for @code{Rterm.exe}.
If the named file does not exist it sets the working directory
if the parent directory exists.)
The following additional command-line options are available when
invoking @code{RGui.exe}.
......
......@@ -2744,11 +2744,11 @@ decisions.
@node X11(), windows(), Specific devices, Specific devices
@subsubsection X11()
The @code{X11()} device dates back to the mid 1990's and was written
then in @code{Xlib}, the most basic X11 toolkit. It has since
optionally made use of a few features from other toolkits: @code{libXt} is
used to read X11 resources, and @code{libXmu} is used in the handling of
clipboard selections.
The @code{X11(type="Xlib")} device dates back to the mid 1990's and was
written then in @code{Xlib}, the most basic X11 toolkit. It has since
optionally made use of a few features from other toolkits: @code{libXt}
is used to read X11 resources, and @code{libXmu} is used in the handling
of clipboard selections.
Using basic @code{Xlib} code makes drawing fast, but is limiting. There
is no support of translucent colours (that came in the @code{Xrender}
......@@ -2791,13 +2791,13 @@ fonts on the machine running @R{} and send grayscale bitmaps to cairo.
@subsubsection windows()
The @code{windows()} device is a family of devices: it supports plotting
to Windows (enhanced) metafiles, @code{BMP}, @code{JPEG} and @code{PNG}
files as well as to Windows printers.
to Windows (enhanced) metafiles, @code{BMP}, @code{JPEG}, @code{PNG} and
@code{TIFF} files as well as to Windows printers.
In most of these cases the primary plotting is to a bitmap: this is used
for the (default) buffering of the screen device, which also enables the
current plot to be saved to BMP, JPEG or PNG (it is the internal bitmap
which is copied to the file in the appropriate format).
current plot to be saved to BMP, JPEG, PNG or TIFF (it is the internal
bitmap which is copied to the file in the appropriate format).
The device units are pixels (logical ones on a metafile device).
......
......@@ -21,7 +21,6 @@ RGUI_CATALOGS = \
RGui-fr.po RGui-fr.gmo \
RGui-it.po RGui-it.gmo \
RGui-ja.po RGui-ja.gmo \
RGui-ko.po RGui-ko.gmo \
RGui-pt_BR.po RGui-pt_BR.gmo \
RGui-ru.po RGui-ru.gmo \
RGui-zh_CN.po RGui-zh_CN.gmo \
......
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......@@ -31,7 +31,7 @@ THE C++ WRAPPER FUNCTIONS
Contributed by: Google Inc.
a Copyright (c) 2007, Google Inc.
Copyright (c) 2007-2008, Google Inc.
All rights reserved.
......
......@@ -5,7 +5,7 @@
/* This is the public header file for the PCRE library, to be #included by
applications that call the PCRE functions.
Copyright (c) 1997-2007 University of Cambridge
Copyright (c) 1997-2008 University of Cambridge
-----------------------------------------------------------------------------
Redistribution and use in source and binary forms, with or without
......@@ -42,9 +42,9 @@ POSSIBILITY OF SUCH DAMAGE.
/* The current PCRE version information. */
#define PCRE_MAJOR 7
#define PCRE_MINOR 6
#define PCRE_MINOR 7
#define PCRE_PRERELEASE
#define PCRE_DATE 2008-01-28
#define PCRE_DATE 2008-05-07
/* When an application links to a PCRE DLL in Windows, the symbols that are
imported have to be identified as such. When building PCRE, the appropriate
......@@ -124,6 +124,7 @@ extern "C" {
#define PCRE_NEWLINE_ANYCRLF 0x00500000
#define PCRE_BSR_ANYCRLF 0x00800000
#define PCRE_BSR_UNICODE 0x01000000
#define PCRE_JAVASCRIPT_COMPAT 0x02000000
/* Exec-time and get/set-time error codes */
......
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......@@ -6,7 +6,7 @@
and semantics are as close as possible to those of the Perl 5 language.
Written by Philip Hazel
Copyright (c) 1997-2007 University of Cambridge
Copyright (c) 1997-2008 University of Cambridge
-----------------------------------------------------------------------------
Redistribution and use in source and binary forms, with or without
......
......@@ -6,7 +6,7 @@
and semantics are as close as possible to those of the Perl 5 language.
Written by Philip Hazel
Copyright (c) 1997-2007 University of Cambridge
Copyright (c) 1997-2008 University of Cambridge
-----------------------------------------------------------------------------
Redistribution and use in source and binary forms, with or without
......@@ -1148,11 +1148,11 @@ for (;;)
do ecode += GET(ecode,1); while (*ecode == OP_ALT);
break;
/* BRAZERO and BRAMINZERO occur just before a bracket group, indicating
that it may occur zero times. It may repeat infinitely, or not at all -
i.e. it could be ()* or ()? in the pattern. Brackets with fixed upper
repeat limits are compiled as a number of copies, with the optional ones
preceded by BRAZERO or BRAMINZERO. */
/* BRAZERO, BRAMINZERO and SKIPZERO occur just before a bracket group,
indicating that it may occur zero times. It may repeat infinitely, or not
at all - i.e. it could be ()* or ()? or even (){0} in the pattern. Brackets
with fixed upper repeat limits are compiled as a number of copies, with the
optional ones preceded by BRAZERO or BRAMINZERO. */
case OP_BRAZERO:
{
......@@ -1174,6 +1174,14 @@ for (;;)
}