Commit 912b894c authored by Dirk Eddelbuettel's avatar Dirk Eddelbuettel

Import Upstream version 2.6.1

parent 367526ac
......@@ -6,6 +6,124 @@
**************************************************
CHANGES IN R VERSION 2.6.1
NEW FEATURES
o The "data.frame" and "factor" methods for [[ now support
the 'exact' argument introduced in 2.6.0.
o plot.lm() gains a new argument 'cex.caption' to allow the
size of the captions to be controlled.
o A series of changes make the CHARSXP cache introduced in 2.6.0
faster (and in some cases many times faster) in sessions with
a large number (e.g. a million) of unique character strings,
and also if there are many empty strings.
o embedFonts(), bitmap() and dev2bitmap() explicitly turn off
auto-rotation in Ghostscript when generating PDF.
o The canonical architecture is no longer checked when loading
packages using a non-empty sub-architecture, since it is
possible to (e.g.) build packages for i386-pc-linux-gnu on both
that architecture and on x86_64-unknown-linux-gnu.
o Deparsing will (if option warnIncomplete is set) warn on
strings longer than the parser limit (8192 bytes).
o url() now uses the UserAgent header in http transactions in
the same way as download.file() (making use of option
"HTTPUserAgent").
BUG FIXES
o iconv() is again able to translate character strings with
embedded nuls (such as those in UCS-2).
o new.packages() and update.packages() failed when called on an
empty library, since old.packages() threw an error.
old.packages() now returns NULL (as documented) in that case.
o Builds on Mac OS X 10.4 or higher now allocate enough space
in the binary headers to relocate dependent libraries into the
framework.
o R CMD build now computes the exclusion list on the copy it
makes: this avoids problems if the original sources contain
symbolic links (which are resolved in the copy). Thanks to
Michael Lawrence for diagnosis and patch.
o object.size() had slightly too low a size for objects of type "S4".
o symbol() in plotmath expressions was only accepting valid
character strings, which made it impossible to specify symbols
such as aleph (obtained by symbol("\300")) in a UTF-8 locale.
o An event handling issue caused autorepeat functions to
misbehave with tcltk (notably scrollbars).
o plot(sin, -5, 5) gives ylab 'sin(x)' again, where it resulted
in 'x(x)' in 2.6.0. Further, plot(sin) again plots from
[0,1] also in cases where a previously used coordinate system
differs.
o curve() with unspecified 'from', 'to' and 'xlim' now reuses the
previous x limits, and not slightly larger ones.
o It was intended that R code filenames in packages should start
with an ASCII letter or digits (and R CMD INSTALL uses that),
but the test used in R CMD build ([A-Za-z0-9]) was
locale-specific (and excluded t to y in Estonian, for
example). (PR#10351)
o 'R CMD build' could misbehave when faced with files with CRLF
line endings *and* no line ending on the final line of the
file, removing the last byte of the file.
o DF[i, j] failed in 2.6.0 if j was a logical vector selecting a
single column.
o Unix x11() would fail if a valid 'display' was specified but
DISPLAY was unset. (PR#10379)
o postscript() was not always ignoring .Postscript.Options in
the workspace (where it should not have occurred).
o help.search() would give an error if it found a badly
installed package, even if 'package' was not specified.
o tclServiceMode() (package tcltk) now works under Unix-alikes.
(Although documented, it used only to work under Windows.)
o As Mac OS X 10.5.0 comes with incompatible /bin/sh shell, we
force SHELL=/bin/bash (which is ok) in that case. [Only for
2.6.x: another solution is used in 2.7.0.]
o Deliberately using malformed source attributes no longer
causes deparsing/printing of functions to crash R. (PR#10437)
o R CMD check and R CMD INSTALL now work with (some) directory
names containing spaces.
o choose(n, k) gave incorrect values for negative n and small k.
o plot.ts(x,y) could use wrong default labels; fixed thanks to
Antonio, Fabio di Narzo.
o reshape() got column names out of sync with contents in some
cases; found by Antonio, Fabio Di Narzo.
o ar(x) for short 'x' (i.e. length <= 10) could fail because the
default 'order.max' was >= length(x) which is non-sensical.
o Keyboard events in getGraphicsEvent() could cause stack
imbalance errors (PR#10453)
CHANGES IN R VERSION 2.6.0
......@@ -100,6 +218,7 @@ NEW FEATURES
o duplicated() and unique() and their methods in base gain an
additional argument 'fromLast'.
o fifo() no longer has a default 'description' argument.
fifo("") is now implemented, and works in the same way as file("").
......@@ -214,9 +333,6 @@ NEW FEATURES
o setRepositories() has a new argument 'ind' to allow selections
to be made programmatically.
o showMethods() has a "smart" default for 'inherited' such that
showMethods(<genfun>, incl = TRUE) becomes a useful short cut.
o sprintf() no longer has a output string length limit.
o storage.mode<- is now primitive, and hence makes fewer copies
......@@ -318,7 +434,7 @@ NEW FEATURES
written by Seth Falcon.
o The internal equivalents of as.complex, as.double, as.integer
and as.logical used to handle length-1 arguments now accept
and as.logical used to handle length=1 arguments now accept
character strings (rather than report that this is
'unimplemented').
......@@ -417,6 +533,9 @@ METHODS PACKAGE
define a new generic with the name of a primitive function
(but having no connection with the primitive).
o showMethods() has a "smart" default for 'inherited' such that
showMethods(<genfun>, incl = TRUE) becomes a useful short cut.
DEPRECATED & DEFUNCT
......@@ -527,10 +646,10 @@ C-LEVEL FACILITIES
o asLogical, asInteger, asReal and asComplex now accept STRSXP
and CHARSXP arguments, and asChar accepts CHARSXP.
o New R_GE_str2col() exported via R_ext/GraphicsEngine.h for
external device developers.
o New entry point R_GE_str2col listed in R_ext/GraphicsEngine.h
for external graphics device developers.
o doKeybd and doMouseevent are now exported in GraphicsDevice.h.
o doKeybd and doMouseevent are now exported in GraphicsDevice.h.
o R_alloc now has first argument of type 'size_t' to support
64-bit platforms (e.g. Win64) with a 32-bit 'long' type.
......@@ -721,7 +840,7 @@ BUG FIXES
PR#9902 by John Brzustowski.
o de.restore() gave a spurious warning for matrices (Ben Bolker)
o plot(fn, xlim=c(a,b)) would not set "from" and "to" properly
when plotting a function. The argument lists to curve() and
plot.function() have been modified slightly as part of the
......@@ -742,13 +861,13 @@ BUG FIXES
assumed that attached environments named "package:foo" were
package environments, although misguided users could use such
a name in attach().
o spline() and splinefun() with method = "periodic" could return
incorrect results when length(x) was 2 or 3.
o getS3method() could fail if the method name contained a regexp
metacharacter such as "+".
o help(<a character vector>) now uses the name and not the
value of the vector unless it has length exactly one, so
e.g. help(letters) now gives help on 'letters'.
......
Revision: 43063
Last Changed Date: 2007-10-03
Revision: 43537
Last Changed Date: 2007-11-26
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......@@ -90,6 +90,15 @@ case "${host_os}" in
esac
AC_SUBST(R_OSTYPE)
case "${host_os}" in
darwin9*) ## test for bad /bin/sh on Leopard
if test `echo '\eof'` != '\eof'; then
AC_MSG_RESULT([Note: forcing SHELL=/bin/bash, because ${SHELL} is incompatible])
SHELL=/bin/bash
fi
;;
esac
### ** Defaults.
cfile="${srcdir}/config.site"
......@@ -1251,7 +1260,7 @@ case "${host_os}" in
## needs -lgfortran because the sharing is a one-way street
## dylib_undefined_allowed=yes
AC_MSG_CHECKING([whether linker supports dynamic lookup])
shlib_ldflags="-dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress"
shlib_ldflags="-dynamiclib -Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress"
AC_CACHE_VAL([r_cv_has_dynlookup],[
[cat > conftest.c <<EOF
void dummy() { }
......
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......@@ -1308,7 +1308,10 @@ is a repository of information related to @acronym{ODBC}.
@findex .dbf
Windows provides drivers not just for DBMSs but also for Excel (@file{.xls})
spreadsheets, DBase (@file{.dbf}) files and even text files. (The named
applications do @emph{not} need to be installed.)
applications do @emph{not} need to be installed.) There are versions
for Excel 2007 and Access 2007 (go to
@url{http://download.microsoft.com}, select `Office' and search for
`ODBC', which will lead to @file{AccessDatabaseEngine.exe}).
@findex odbcConnect
@findex odbcDriverConnect
......@@ -1424,8 +1427,6 @@ Notice that the specification of the table is different from the name
returned by @code{sqlTables}: @code{sqlFetch} is able to map the
differences.
The ODBC interface to Excel spreadsheets is read-only; you cannot alter
the spreadsheet data.
@c @node RPgSQL, , RODBC, R interface packages
......@@ -2088,9 +2089,11 @@ project at @url{http://www.omegahat.org/RSCORBA/}.
@node Reading Excel spreadsheets, References, Network interfaces, Top
@chapter Reading Excel spreadsheets
The most common R data import/export question seems to be `how do I read an
Excel spreadsheet'. This chapter collects together advice and options
given earlier.
The most common R data import/export question seems to be `how do I read
an Excel spreadsheet'. This chapter collects together advice and
options given earlier. Note that most of the advice is for pre-Excel
2007 spreadsheets: currently the only one of these methods that reads
the @file{.xlsx} format is that @emph{via} @pkg{RODBC}.
@findex read.csv
@findex read.delim
......@@ -2109,10 +2112,11 @@ If you do not have Excel, many other programs are able to read such
spreadsheets and export in a text format on both Windows and Unix, for
example Gnumeric (@url{http://www.gnome.org/projects/gnumeric/}) and
OpenOffice (@url{http://www.openoffice.org}). You can also
cut-and-paste from the display of a spreadsheet in such a program and R:
@code{read.table} will read from the R console or, under Windows, from
the clipboard (via @code{file = "clipboard"} or @code{readClipboard}).
The @code{read.DIF} function can also read from the clipboard.
cut-and-paste between the display of a spreadsheet in such a program and
R: @code{read.table} will read from the R console or, under Windows,
from the clipboard (via @code{file = "clipboard"} or
@code{readClipboard}). The @code{read.DIF} function can also read from
the clipboard.
Note that an Excel @file{.xls} is not just a spreadsheet: such files can
contain many sheets, and the sheets can contain formulae, macros and so
......@@ -2120,9 +2124,12 @@ on. Not all readers can read other than the first sheet, and may be
confused by other contents of the file.
@findex odbcConnectExcel
@findex odbcConnectExcel2007
Windows users can use @code{odbcConnectExcel} in package @pkg{RODBC}.
This can select rows and columns from any of the sheets in an Excel
spreadsheet file.
spreadsheet file. The version @code{odbcConnectExcel2007} will read the
Excel 2007 formats as well as earlier ones (provided the latest drivers
are installed: see above).
@findex xlsReadWrite
Also only for Windows, the package @pkg{xlsReadWrite} has a function
......
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......@@ -6940,9 +6940,9 @@ value accepted is 100000.
(Windows only) Specify a limit for the amount of memory to be used both
for @R{} objects and working areas. This is set by default to the
smaller of 1.5Gb@footnote{2.5Gb on versions of Windows that support 3Gb
per process and have the support enabled: see the @file{rw-FAQ} Q2.9.}
and the amount of physical RAM in the machine, and must be between 32Mb
and 3Gb.
per process and have the support enabled: see the @file{rw-FAQ} Q2.9;
3.5Gb on some 64-bit versions of Windows.} and the amount of physical
RAM in the machine, and must be between 32Mb and 3Gb.
@item --quiet
@itemx --silent
......
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Name: GNU General Public License
Abbrev: GPL
Version: 2
SSS: GPL-2
OSF: open
FSF: free_and_GPL_compatible
URL: http://www.R-project.org/Licenses/GPL-2
Name: GNU General Public License
Abbrev: GPL
Version: 3
SSS: GPL-3
OSF: open
FSF: free_and_GPL_compatible
URL: http://www.R-project.org/Licenses/GPL-3
Name: GNU Library General Public License
Abbrev: LGPL
Version: 2
SSS: LGPL-2
OSF: open
FSF: free_and_GPL_compatible
URL: http://www.R-project.org/Licenses/LGPL-2
Name: GNU Lesser General Public License
Abbrev: LGPL
Version: 2.1
SSS: LGPL-2.1
OSF: open
FSF: free_and_GPL_compatible
URL: http://www.R-project.org/Licenses/LGPL-2.1
Name: GNU Lesser General Public License
Abbrev: LGPL
Version: 3
SSS: LGPL-3
OSF: open
FSF: free_and_GPL_compatible
URL: http://www.R-project.org/Licenses/LGPL-3
Name: Apache License
Version: 1.0
OSF: open
FSF: free_and_GPL_incompatible
URL: http://www.apache.org/LICENSE-1.0
Name: Apache License
Version: 1.1
OSF: open
FSF: free_and_GPL_incompatible
URL: http://www.apache.org/LICENSE-1.1
Name: Apache License
Version: 2.0
OSF: open
FSF: free_and_GPL_compatible
URL: http://www.apache.org/licenses/LICENSE-2.0
Name: Artistic License
Version: 1.0
SSS: Artistic-1.0
OSF: open
FSF: non_free
URL: http://www.R-project.org/Licenses/Artistic-1.0
Name: Artistic License
Version: 2.0
SSS: Artistic-2.0
OSF: open
FSF: free_and_GPL_compatible
URL: http://www.R-project.org/Licenses/Artistic-2.0
Name: CeCILL
Abbrev: CeCILL
Version: 2
FSF: free_and_GPL_compatible
URL: http://www.cecill.info/licences.en.html
Name: FreeBSD License
Abbrev: FreeBSD
FSF: free_and_GPL_compatible
URL: http://www.freebsd.org/copyright/freebsd-license.html
Name: MIT License
Abbrev: MIT
OSF: open
URL: http://www.opensource.org/licenses/mit-license.php
Name: Modified BSD License
Abbrev: BSD
OSF: open
FSF: free_and_GPL_compatible
URL: http://www.opensource.org/licenses/bsd-license.php
Name: Mozilla Public License
Abbrev: MPL
Version: 1.0
OSF: open
FSF: free_and_GPL_incompatible
URL: http://www.opensource.org/licenses/mozilla1.0.php
Name: Mozilla Public License
Abbrev: MPL
Version: 1.1
OSF: open
FSF: free_and_GPL_incompatible
URL: http://www.opensource.org/licenses/mozilla1.1.php
Name: X11 License
Abbrev: X11
FSF: free_and_GPL_compatible
URL: http://www.xfree86.org/3.3.6/COPYRIGHT2.html#3
......@@ -3,10 +3,11 @@ get_dcf_field () {
## Usage:
## get_dcf_field FIELD FILE
ws="[ ]" # space and tab
(sed -n "/^${1}:/,/^[^ ]/{p;}" ${2} | \
sed -n "/^${1}:/{s/^${1}:${ws}*//;p;}
/^${ws}/{s/^${ws}*//;p;}") |
sed "s/[ ]*$//"
${SED-sed} -n "/^${1}:/,/^[^ ]/p" ${2} | \
${SED-sed} -n "1s/^${1}:${ws}*//p; /^${ws}/p" | \
${SED-sed} "/^${ws}/s/^${ws}*//; s/[ ]*$//"
## (Strip leading tag [first match], delete all additional tag
## lines, and remove leading whitespace from continuation lines.)
}
### Local Variables: ***
......
......@@ -9,6 +9,45 @@
**************************************************
CHANGES IN R VERSION 2.6.0 patched
PACKAGE INSTALLATION
o Fortran code in packages is no longer compiled with -Wall, as
this is not done on other platforms.
OTHERS
o The canvas used when plotting on a jpeg() or bmp() device with
a transparent background (most often by copying from a screen
device with the default transparent background) is now white
and not grey.
o It seems file.access() can be unreliable both ways: that is it
can also report that access is barred when it is not.
(Seen on network file systems.) So install.packages() to a
single library no longer makes use of file.access() but checks
directory creation instead: it is still possible that you can
create a directory but not be allowed to create a .dll or .chm
file, at least under Vista.
o When R_COMPLETION is set to FALSE, TAB is no longer ignored,
but advances to the next tab stop in Rterm (the pre-2.5.0
behaviour) and inserts a space in Rgui.
BUG FIXES
o Saving a plot to Postscript or PDF required the font database
to have been initialized: this is now done if necessary.
o Very long file or pathnames could cause a crash if opened in
the script editor. (PR#10402)
CHANGES IN R VERSION 2.6.0
GUI CHANGES
......@@ -42,9 +81,10 @@ FUNCTION CHANGES
o l10n_info() reports the codepage in current use.
o dQuote() and sQuote() now use directional quotes by
default. You might prefer options(useFancyQuotes=FALSE) when
running Rterm.
o dQuote() and sQuote() now use directional quotes by default
under RGui. You might prefer options(useFancyQuotes=FALSE)
if the console font does not have these quotes: see the
rw-FAQ.
INSTALLER
......@@ -185,8 +225,8 @@ BUG FIXES
o .Platform$GUI would report "Rgui" when no GUI was present in
R(D)COM.
o '=' within -e expression is no longer interpreted as setting
an environment variable.
o '=' within '-e expression' on the command line is no longer
interpreted as setting an environment variable.
......@@ -206,7 +246,7 @@ GUI CHANGES
or debug sessions.
o Using a modal widget from Rterm (e.g. select.list) is now far
likely to be forced to the front.
more likely to be forced to the front.
OTHERS
......@@ -256,7 +296,7 @@ BUG FIXES
o winMenuDel() was not automatically deleting sub-menus when a
user menu was deleted. (PR#9702)
o Rcnd INSTALL --docs=txt etc works (for a single type, except
o Rcmd INSTALL --docs=txt etc works (for a single type, except
'chm' which is equivalent to 'all' nowadays).
......@@ -955,7 +995,7 @@ UNCATEGORIZED
registry entry
HKEY_LOCAL_MACHINE\Software\R-core\R\{version}\InstallPath
will be added. Users require administrative privileges to
create this key. For others, the same key will be put under
create this key: for others, the same key will be put under
the HKEY_CURRENT_USER root.
o The sample R_HOME/etc/Rprofile file has been renamed to
......
......@@ -42,20 +42,20 @@ endif
ifdef DEBUG
DLLFLAGS=
DEBUGFLAG=$(G_FLAG) -Wall
DEBUGFLAG=$(G_FLAG)
else
DLLFLAGS=-s
DEBUGFLAG=-Wall
DEBUGFLAG=
endif
COPTFLAG=-O3
CXXOPTFLAG=-O2
COPTFLAG=-O3 -Wall
CXXOPTFLAG=-O2 -Wall
FOPTFLAG=-O3
CPPFLAGS=$(PKG_CPPFLAGS) -I$(RHOME)/include $(CLINK_CPPFLAGS)
CFLAGS=$(PKG_CFLAGS) $(DEBUGFLAG) $(COPTFLAG)
CXXFLAGS=$(PKG_CXXFLAGS) $(DEBUGFLAG) $(CXXOPTFLAG)
FFLAGS=$(PKG_FFLAGS) $(FOPTFLAG) $(DEBUGFLAG)
FFLAGS=$(PKG_FFLAGS) $(DEBUGFLAG) $(FOPTFLAG)
DLLLIBS=-L$(RHOME)/$(IMPDIR) $(PKG_LIBS) $(PKG_LIBS2) $(EXTRA_LIBS) -lR
RESFLAGS=-I $(RHOME)/include
......
......@@ -32,7 +32,7 @@ LEA_MALLOC=YES
USE_ATLAS=NO