[R] R-2.1.0 is released
Peter Dalgaard
p.dalgaard at biostat.ku.dk
Mon Apr 18 14:36:11 CEST 2005
I've rolled up R-2.1.0.tar.gz a short while ago. This version contains
several substantial changes and additions, perhaps most notably the
UTF8 and Internationalization changes. See the full list of changes
below.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.1.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.
There is also a version split for floppies (does anyone use these any
more?).
For the R Core Team
Peter Dalgaard
These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:
94d55d512a9ba36caa9b7df079bae19f COPYING
d8045f3b8f929c1cb29a1e3fd737b499 COPYING.LIB
70447ae7f2c35233d3065b004aa4f331 INSTALL
8b78e12b100a6834fdada2dfaab98ab0 NEWS
88bbd6781faedc788a1cbd434194480c ONEWS
4f004de59e24a52d0f500063b4603bcb OONEWS
e7f92ef0c2bc5b772a83f42a5ed504c9 R-2.1.0.tar.gz
d45b1084f91fcfeebbb69cc2dd9ed6e1 R-2.1.0.tar.gz-split.aa
18b34d82302a68a86510da6e0dd9a193 R-2.1.0.tar.gz-split.ab
d242b365ed1398031ff26d31a6da9c1c R-2.1.0.tar.gz-split.ac
b992e7d10baf662ede52a0c156f51d86 R-2.1.0.tar.gz-split.ad
a2c559b4b1c87f5815bec9e8e2b7bd31 R-2.1.0.tar.gz-split.ae
033ae9f596d74f9780f98c9b6cab31df R-2.1.0.tar.gz-split.af
ed0fd6939e8e84b0a4a2a01d92cc7f96 R-2.1.0.tar.gz-split.ag
2d1379175456b308328d9af09e2726a3 R-2.1.0.tar.gz-split.ah
bbb8fd837e27c931b9921548ee4c5c28 R-2.1.0.tar.gz-split.ai
e7f92ef0c2bc5b772a83f42a5ed504c9 R-latest.tar.gz
56a780cdec835c5c598f8dfc0738f7f3 README
Here is the relevant bit of the NEWS file:
CHANGES IN R VERSION 2.1.0
USER-VISIBLE CHANGES
o box plots {by boxplot() or bxp()} now have the median line three
times the normal line width in order to distinguish it from the
quartile ones.
o Unix-alike versions of R can now be used in UTF-8 locales on
suitably equipped OSes. See the internationalization section
below.
o The meaning of 'encoding' for a connection has changed: See the
internationalization section below.
o There has been some rationalization of the format of
warning/error messages, to make them easier to translate.
Generally names of functions and arguments are single-quoted,
and classes double-quoted.
o Reading text files with embedded "\" (as in Windows file names)
may now need to use scan(* , allowEscapes = FALSE), see also below.
NEW FEATURES
o %% now warns if its accuracy is likely to be affected by lack
of precision (as in 1e18 %% 11, the unrealistic expectation of
PR#7409), and tries harder to return a value in range when it is.
o abbreviate() now warns if used with non-ASCII chars, as the
algorithm is designed for English words.
o The default methods for add1() and drop1() check for changes
in the number of cases in use.
The "lm" and "glm" methods for add1() quoted the <none> model
on the original fitted values when using (with a warning) a
smaller set of cases for the expanded models.
o Added alarm() function to generate a bell or beep or visual alert.
o all/any() now attempt to coerce their arguments to logical, as
documented in the Blue Book. This means e.g. any(list()) works.
o New functions for multivariate linear models: anova.mlm(),
SSD(), estVar(), mauchley.test() (for sphericity).
vcov() now does something more sensible for "mlm" class objects.
o as.data.frame.table() has a new argument 'responseName'
(contributed by Bill Venables).
o as.dist() and cophenetic() are now generic, and the latter has a
new method for objects of class "dendrogram".
o as.ts() is now generic.
o binomial() has a new "cauchit" link (suggested by Roger Koenker).
o chisq.test() has a new argument 'rescale.p'. It is now possible
to simulate (slowly) the P value also in the 1D case
(contributed by Rolf Turner).
o choose(n,k) and lchoose(.) now also work for arbitrary (real) n
in accordance with the general binomial theorem. choose(*,k)
is more accurate (and faster) for small k.
o Added colorRamp() and colorRampPalette() functions for color
interpolation.
o colSums()/rowSums() now allow arrays with a zero-length extent
(requested by PR#7775).
o confint() has stub methods for classes "glm" and "nls" that
invoke those in package MASS. This avoids using the "lm"
method for "glm" objects if MASS is not attached.
confint() has a default method using asymptotic normality.
o contr.SAS() has been moved from the 'nlme' package to the
'stats' package.
o New function convertColors() maps between color spaces.
colorRamp() uses it.
o The cov() function in the non-Pearson cases now ranks data after
removal of missing values, not before. The pairwise-complete
method should now be consistent with cor.test. (Code
contributed by Shigenobu Aoki.)
o Added delayedAssign() function to replace delay(), which is now
deprecated.
o dir.create() has a new argument 'recursive' serving the same
purpose as Unix's mkdir -p.
o do.call() now takes either a function or a character string as
its first argument. The supplied arguments can optionally be
quoted.
o duplicated() and unique() now accept "list" objects, but are
fast only for simple list objects.
o ecdf() now has jumps of the correct size (a multiple of 1/n)
if there are ties. (Wished by PR#7292).
o eff.aovlist() assumed orthogonal contrasts for any term
with more than one degree of freedom: this is now documented
and checked for. Where each term only occurs in only one
stratum the efficiencies are all one: this is detected and
orthogonal contrasts are not required.
o New function encodeString() to encode character strings in the
same way that printing does.
o file("clipboard") now work for reading the primary selection on
Unix-alikes with an active X11 display. (It has long worked
for reading and writing under Windows.) The secondary
selection can also be read: see ?file.
file() now allows mode "w+b" as well as "w+".
o file.append() has been tuned, including for the case of
appending many files to a single file.
o Functions flush.console() and select.list() are now available
on all platforms. There is a Tcl/Tk-based version of
select.list() called tk_select.list() in package tcltk.
o gc() now reports maximum as well as current memory use.
o A new function getGraphicsEvent() has been added which will allow
mouse or keyboard input from a graphics device. (NB: currently
only the Windows screen device supports this function. This
should improve before the 2.1.0 release.)
o New functions gray.colors()/grey.colors() for gray color
palettes.
o grep(), gsub(), sub() and regexpr() now always attempt to
coerce their 'pattern', 'x', 'replacement' and 'text'
arguments to character. Previously this was undocumented but
done by [g]sub() and regexpr() for some values of their
other arguments. (Wish of PR#7742.)
o gsub/sub() have a new 'fixed' method.
o New function hcl() for creating colors for a given hue,
chroma and luminance (i.e. perceptual hsv).
o isTRUE() convenience function to be used for programming.
o kmeans() now returns an object of class "kmeans" which has a
print() method.
Two alternative algorithms have been implemented.
If the number of centres is supplied, it has a new option of
multiple random starts.
o The limits on the grid size in layout() are now documented, and
have been raised somewhat by using more efficient internal
structures.
o legend() now accepts positioning by keyword, e.g. "topleft",
and can put a title within the legend. (Suggested by Elizabeth
Purdom in PR#7400.)
o mahalanobis() now has a '...' argument which is passed to solve()
for computing the inverse of the covariance matrix, this replaces
the former 'tol.inv' argument.
o menu() uses a multi-column layout if possible for more than
10 choices.
menu(graphics = TRUE) is implemented on most platforms via
select.list() or tk_select.list().
o New function message() in 'base' for generating "simple"
diagnostic messages, replacing such a function in the
'methods' package.
o na.contiguous() is now (S3) generic with first argument
renamed to 'object'.
o New function normalizePath() to find canonical paths (and on
Windows, canonical names of components).
o The default in options("expressions") has been increased to 5000,
and the maximal settable value to 500000.
o p.adjust() has a new method "BY".
o pbeta() now uses a different algorithm for large values of at
least one of the shape parameters, which is much faster and is
accurate and reliable for very large values. (This affects
pbinom(), pf(), qbeta() and other functions using pbeta at C
level.)
o pch="." now by default produces a rectangle at least 0.01" per
side on high-resolution devices. (It used to be one-pixel
square even on high-resolution screens and Windows printers,
but 1/72" on postscript() and pdf() devices.) Additionally,
the size is now scalable by 'cex'; see ?points and note that
the details are subject to change.
o pdf() now responds to the 'paper' and 'pagecentre'
arguments. The default value of 'paper' is "special"
for backward-compatibility (this is different from the
default for postscript()).
o plot.data.frame() tries harder to produce sensible plots for
non-numeric data frames with one or two columns.
o The predict() methods for "prcomp" and "princomp" now match
the columns of 'newdata' to the original fit using column
names if these are available.
o New function recordGraphics() to encapsulate calculations
and graphics output together on graphics engine display list.
To be used with care.
o New function RSiteSearch() to query R-related resources
on-line (contributed by Jonathan Baron and Andy Liaw).
o scan() arranges to share storage of duplicated character
strings read in: this can dramatically reduce the memory
requirements for large character vectors which will
subsequently be turned into factors with relatively few
levels. For a million items this halved the time and reduced
storage by a factor of 20.
scan() has a new argument 'allowEscapes' (default TRUE) that
controls when C-style escapes in the input are interpreted.
Previously only \n and \r were interpreted, and then only
within quoted strings when no separator was supplied.
scan() used on an open connection now pushes back on the
connection its private `ungetc' and so is safer to use to
read partial lines.
o scatter.smooth() and loess.smooth() now handle missing values
in their inputs.
o seq.Date() and seq.POSIXt() now allow 'to' to be before 'from'
if 'by' is negative.
o sprintf() has been enhanced to allow the POSIX/XSI specifiers
like "%2$6d", and also accepts "%x" and "%X".
sprintf() does limited coercion of its arguments.
sprintf() accepts vector arguments and operates on them in
parallel (after re-cycling if needed).
o New function strtrim() to trim character vectors to a display
width, allowing for double-width characters in multi-byte
character sets.
o subset() now has a method for matrices, similar to that for
data frames.
o Faster algorithm in summaryRprof().
o sunflowerplot() has new arguments 'col' and 'bg'.
o sys.function() now has argument 'which' (as has long been
presaged on its help page).
o Sys.setlocale("LC_ALL", ) now only sets the locale categories
which R uses, and Sys.setlocale("LC_NUMERIC", ) now gives a
warning (as it can cause R to malfunction).
o unclass() is no longer allowed for environments and external
pointers (since these cannot be copied and so unclass() was
destructive of its argument). You can still change the
"class" attribute.
o File-name matching is no longer case-insensitive with unz()
connections, even on Windows.
o New argument 'immediate.' to warning() to send an immediate
warning.
o New convenience wrappers write.csv() and write.csv2().
o There is a new version for write.table() which is implemented in C.
For simple matrices and data frames this is several times
faster than before, and uses negligible memory compared to the
object size.
The old version (which no longer coerces a matrix to a data
frame and then back to a matrix) is available for now as
write.table0().
o The functions xinch(), yinch(), and xyinch() have been moved
from package 'grDevices' into package 'graphics'.
o Plotmath now allows underline in expressions. (PR#7286,
contributed by Uwe Ligges.)
o BATCH on Unix no longer sets --gui="none" as the X11 module
is only loaded if needed.
o The X11 module (and the hence X11(), jpeg() and png() devices
and the X-based dataentry editor) is now in principle
available under all Unix GUIs except --gui="none", and this is
reflected in capabilities().
capabilities("X11") determines if an X server can be accessed,
and so is more likely to be accurate.
o Printing of arrays now honours the 'right' argument if there
are more than two dimensions.
o Tabular printing of numbers now has headers right-justified, as
they were prior to version 1.7.0 (spotted by Rob Baer).
o Lazy-loading databases are now cached in memory at first use:
this enables R to run much faster from slow file systems such
as USB flash drives. There is a small (less than 2Mb)
increase in default memory usage.
o The implicit class structure for numeric vectors has been
changed, so that integer/real vectors try first methods for
class "integer"/"double" and then those for class "numeric".
The implicit classes for matrices and arrays have been changed
to be "matrix"/"array" followed by the class(es) of the
underlying vector.
o splines::splineDesign() now allows the evaluation of a B-spline
basis everywhere instead of just inside the "inner" knots, by
setting the new argument `outer.ok = TRUE'.
o Hashing has been tweaked to use half as much memory as before.
o Readline is not used for tilde expansion when R is run with
--no-readline, nor from embedded applications. Then "~name"
is no longer expanded, but "~" still is.
o The regular expression code is now based on that in glibc 2.3.3.
It has stricter conformance to POSIX, so metachars such as
{ } + * may need to be escaped where before they did not
(but could have been).
o New encoding 'TeXtext.enc' improves the way postscript() works
with Computer Modern fonts.
o Replacement in a non-existent column of a data frame tries
harder to create a column of the correct length and so avoid a
corrupt data frame.
o For Windows and readline-based history, the saved file size is
re-read from R_HISTSIZE immediately before saving.
o Collected warnings during start-up are now printed before the
initial prompt rather than after the first command.
o Changes to package 'grid':
- preDrawDetails(), drawDetails(), and postDrawDetails()
methods are now recorded on the graphics engine
display list. This means that calculations within these
methods are now run when a device is resized or
when output is copied from one device to another.
- Fixed bug in grid.text() when 'rot' argument has length 0.
(privately reported by Emmanuel Paradis)
- New getNames() function to return just the names of all top-level
grobs on the display list.
- Recording on the grid display list is turned off within
preDrawDetails(), drawDetails(), and postDrawDetails() methods.
- Grid should recover better from errors or user-interrupts
during drawing (i.e., not leave you in a strange viewport
or with strange graphical parameter settings).
- New function grid.refresh() to redraw the grid display list.
- New function grid.record() to capture calculations
with grid graphics output.
- grobWidth and grobHeight ("grobwidth" and "grobheight" units)
for primitives (text, rects, etc, ...) are now
calculated based on a bounding box for the relevant grob.
NOTE: this has changed the calculation of the size of a scalar
rect (or circle or lines).
- New arguments 'warn' and 'wrap' for function grid.grab()
- New function grid.grabExpr() which captures the output from
an expression (i.e., not from the current scene) without
doing any drawing (i.e., no impact on the current scene).
- upViewport() now (invisibly) returns the path that it goes up
(suggested by Ross Ihaka).
- The 'gamma' gpar has been deprecated (this is a device property
not a property of graphical objects; suggested by Ross Ihaka).
- New 'lex' gpar; a line width multiplier.
- grid.text() now handles any language object as mathematical
annotation (instead of just expressions).
- plotViewport() has default value for 'margins' argument (that match
the default value for par(mar)).
- The 'extension' argument to dataViewport() can now be vector,
in which case the first value is used to extend the xscale and
the second value is used to extend the y scale.
(suggested by Ross Ihaka).
- All 'just' arguments (for viewports, layouts, rectangles, text)
can now be numeric values (typically between 0 [left] and 1 [right])
as well as character values ("left", "right", ...).
For rectangles and text, there are additional 'hjust' and 'vjust'
arguments which allow numeric vectors of justification in
each direction (e.g., so that several pieces of text can have
different justifications).
(suggested by Ross Ihaka)
- New 'edits' argument for grid.xaxis() and grid.yaxis() to
allow specification of on-the-fly edits to axis children.
- applyEdit(x, edit) returns x if target of edit (i.e., child
specified by a gPath) cannot be found.
- Fix for calculation of length of max/min/sum unit. Length is
now (correctly) reported as 1 (was reported as length of first arg).
- Viewport names can now be any string (they used to have to be a
valid R symbol).
- The 'label' argument for grid.xaxis() and grid.yaxis() can now
also be a language object or string vector, in which case it
specifies custom labels for the tick marks.
INTERNATIONALIZATION
o Unix-alike versions of R can now be used in UTF-8 and other
multi-byte locales on suitably equipped OSes if configured
with option --enable-mbcs (which is the default). [The
changes to font handling in the X11 module are based on the
Japanization patches of Eiji Nakama.]
Windows versions of R can be used in `East Asian' locales on
suitable versions of Windows.
See the 'Internationalization' chapter in the 'Installation
and Administration' manual.
o New command-line flag --encoding to specify the encoding to
be assumed for stdin (but not for a console).
o New function iconv() to convert character vectors between
encodings, on those OSes which support this. See the new
capabilities("iconv").
o The meaning of 'encoding' for a connection has changed: it now
allows any charset encoding supported by iconv on the
platform, and can re-encode output as well as input.
As the new specification is a character string and the old was
numeric, this should not cause incorrect operation.
o New function localeToCharset() to find/guess encoding(s) from
the locale name.
o nchar() returns the true number of bytes stored (including any
embedded nuls), this being 2 for missing values. It has an
optional argument 'type' with possible non-default values
"chars" and "width" to give the number of characters or the
display width in columns.
o Characters can be entered in hexadecimal as e.g. \x9c, and in
UTF-8 and other multibyte locales as \uxxxx, \u{xxxx},
\Uxxxxxxxx or \U{xxxxxxxx}. Non-printable Unicode characters
are displayed C-style as \uxxxx or \Uxxxxxxxx.
o LC_MONETARY is set to the locale, which affects the result of
Sys.localeconv(), but nothing else in R itself. (It could
affect add-on packages.)
o source() now has an 'encoding' argument which can be used to
make it try out various possible encodings. This is made use
of by example() which will convert (non-UTF-8) Latin-1 example
files in a UTF-8 locale.
o read/writeChar() work in units of characters, not bytes.
o .C() now accepts an ENCODING= argument where re-encoding is
supported by the OS. See `Writing R Extensions'.
o delimMatch (tools) now reports match positions and lengths in
units of characters, not bytes. The delimiters can be
strings, not just single ASCII characters.
o .Rd files can indicate via a \encoding{} argument the encoding
that should be assumed for non-ASCII characters they contain.
o Phrases in .Rd files can be marked by \enc{}{} to show a
transliteration to ASCII for use in e.g. text help.
o The use of 'pch' in points() now allows for multi-byte character
sets: in such a locale a glyph can either be specified as a
multi-byte single character or as a number, the Unicode point.
o New function l10n_info() reports on aspects of the
locale/charset currently in use.
o scan() is now aware of double-byte locales such as Shift-JIS
in which ASCII characters can occur as the second ('trail')
byte.
o Functions sQuote() and dQuote() use the Unicode directional
quotes if in a UTF-8 locale.
o The infrastructure is now in place for C-level error and warning
messages to be translated and used on systems with Native
Language Support. This has been used for the startup message
in English and to translate Americanisms such as 'color' into
English: translations to several other languages are under
way, and some are included in this release.
See 'Writing R Extensions' for how to make use of this in a
package: all the standard packages have been set up to do
translation, and the 'language' 'en at quot' is implemented to
allow Unicode directional quotes in a UTF-8 locale.
o R-level stop(), warning() and message() messages can be
translated, as can other messages via the new function
gettext(). Tools xgettext() and xgettext2pot() are provided in
package tools to help manage error messages.
gettextf() is a new wrapper to call sprintf() using
gettext() on the format string.
o Function ngettext() allows the management of singular and
plural forms of messages.
UTILITIES
o New functions mirror2html() and checkCRAN().
o R CMD check has a new option '--use-valgrind'.
o R CMD check now checks that Fortran and C++ files have LF
line endings, as well as C files. It also checks Makevars[.in]
files for portable compilation flags.
o R CMD check will now work on a source tarball and prints out
information about the version of R and the package.
o tools:::.install_package_code_files() (used to collate R files
when installing packages) ensures files are separated by a
line feed.
o vignette() now returns an object of class "vignette" whose
print() method opens the corresponding PDF file. The edit()
method can be used to open the code of the vignette in an
editor.
o R CMD INSTALL on Unix has a new option '--build' matching
that on Windows, to package as tarball the installed package.
o R CMD INSTALL on Unix can now install binary bundles.
o R CMD build now changes src files to LF line endings if necessary.
o R CMD build now behaves consistently between source and binary
builds: in each case it prepares a source directory and then
either packages that directory as a tarball or calls R CMD
INSTALL --build on the prepared sources.
This means that R CMD build --binary now respects
.Rbuildignore and will rebuild vignettes (unless the option
--no-vignettes is used). For the latter, it now installs the
current sources into a temporary library and uses that version
of the package/bundle to rebuild the vignettes.
o R CMD build now reports empty directories in the source tree.
o New function write_PACKAGES() in package 'tools' to help with
preparing local package repositories. (Based on a contribution
by Uwe Ligges.) How to prepare such repositories is
documented in the 'R Installation and Administration' manual.
o package.skeleton() adds a bit more to DESCRIPTION.
o Sweave changes:
- \usepackage[nogin]{Sweave} in the header of an Sweave file
supresses auto-setting of the graphical parameter like width
of graphics.
- The new \SweaveInput{} command works similar to LaTeX's
\input{} command.
- Option value strip.white=all strips all blank lines from the
output of a code chunk.
- Code chunks with eval=false are commented out by Stangle() and
hence no longer tested by R CMD check.
DOCUMENTATION
o File doc/html/faq.html no longer exists, and doc/manual/R-FAQ.html
(which has active links to other manuals) is used instead.
(If makeinfo >= 4.7 is not available, the version on CRAN is
linked to.)
o Manual 'Writing R Extensions' has further details on writing
new front-ends for R using the new public header files.
o There are no longer any restrictions on characters in the
\name{} field of a .Rd file: in particular _ is supported.
C-LEVEL FACILITIES
o There are new public C/C++ header files Rinterface.h and
R_ext/RStartup.h for use with external GUIs.
o Added an onExit() function to graphics devices, to be executed
upon user break if non-NULL.
o ISNAN now works even in C++ code that undefines the 'isnan' macro.
o R_alloc's limit on 64-bit systems has been raised from just
under 2^31 bytes (2Gb) to just under 2^34 (16Gb), and is now checked.
o New math utility functions log1pmx(x), lgamma1p(x),
logspace_add(logx, logy), and logspace_sub(logx, logy).
DEPRECATED & DEFUNCT
o The aqua module for MacOS X has been removed: --with-aqua now
refers to the unbundled Cocoa GUI.
o Capabilities "bzip2", "GNOME, "libz" and "PCRE" are defunct.
o The undocumented use of UseMethod() with no argument was
deprecated in 2.0.1 and is now regarded as an error.
o Capability "IEEE754" is deprecated.
o The 'CRAN' argument to update.packages(), old.packages(),
new.packages(), download.packages() and install.packages() is
deprecated in favour of 'repos', which replaces it as a
positional argument (so this is only relevant for calls with
named args).
o The S3 methods for getting and setting names of "dist" objects
have been removed (as they provided names with a different
length from the "dist" object itself).
o Option "repositories" is no longer used and so not set.
o loadURL() is deprecated in favour of load(url()).
o delay() is deprecated. Use delayAssign() instead.
INSTALLATION CHANGES
o New configure option --enable-utf8 to enable support for
UTF-8 locales, on by default.
o R_XTRA_[CF]FLAGS are now used during the configuration tests,
and [CF]PICFLAGS if --enable-R-shlib was specified. This
ensures that features such as inlining are only used if the
compilation flags specified support them. (PR#7257)
o Files FAQ, RESOURCES, doc/html/resources.html are no longer in
the SVN sources but are made by 'make dist'.
o The GNOME GUI is unbundled, now provided as a package on CRAN.
o Configuring without having the recommended packages is now an
error unless --with-recommended-packages=no (or equivalent) is used.
o Configuring without having the X11 headers and libraries is now
an error unless --with-x=no (or equivalent) is used.
o Configure tries harder to find a minimal set of FLIBS. Under
some circumstances this may remove from R_LD_LIBRARY_PATH
path elements that ought to have specified in LDFLAGS (but
were not).
o The C code for most of the graphics device drivers and their
afm files are now in package grDevices.
o R is now linked against ncurses/termlib/termcap only if
readline is specified (now the default) and that requires it.
o Makeinfo 4.7 or later is now required for building the HTML and
Info versions of the manuals.
PACKAGE INSTALLATION CHANGES
o There are new types of packages, identified by the Type field
in the DESCRIPTION file. For example the GNOME console is now
a separate package (on CRAN), and translations can be
distributed as packages.
o There is now support of installing from within R both source and
binary packages on MacOS X and Windows. Most of the R
functions now have a 'type' argument defaulting to
getOption("pkgType") and with possible values "source",
"win.binary" and "mac.binary". The default is "source" except
under Windows and the CRAN GUI build for MacOS X.
o install.packages() and friends now accept a vector of URLs for
'repos' or 'contriburl' and get the newest available version of
a package from the first repository on the list in which it is
found. The argument 'CRAN' is still accepted, but deprecated.
install.packages() on Unix can now install from local .tar.gz
files via repos = NULL (as has long been done on Windows).
install.packages() no longer asks if downloaded packages
should be deleted: they will be deleted at the end of the
session anyway (and can be deleted by the user at any time).
If the repository provides the information, install.packages()
will now accept the name of a package in a bundle.
If 'pkgs' is omitted install.packages() will use a listbox to
display the available packages, on suitable systems.
'dependencies' can be a character vector to allow only some
levels of dependencies (e.g. not "Suggests") to be requested.
o There is a new possible value update.packages(ask="graphics")
that uses a widget to (de)select packages, on suitable systems.
o The option used is now getOption("repos") not getOption("CRAN")
and it is initially set to a dummy value. Its value can be a
character vector (preferably named) giving one or several
repositories.
A new function chooseCRANmirror() will select a CRAN mirror.
This is called automatically if the contrib.url() encounters
the initial dummy value of getOption("repos")
A new function setRepositories() can be used to create
getOption("repos") from a (platform-specific) list of known
repositories.
o New function new.packages() to report uninstalled packages
available at the requested repositories. This also reports
incomplete bundles. It will optionally install new packages.
o New function available.packages(), similar to CRAN.packages()
but for use with multiple repositories. Both now only report
packages whose R version requirements are met.
o update.packages() and old.packages() have a new option
'checkBuilt' to allow packages installed under earlier
versions of R to be updated.
o remove.packages() can now remove bundles.
o The Contains: field of the DESCRIPTION file of package bundles
is now installed, so later checks can find out if the bundle
is complete.
o packageStatus() is now built on top of *.packages, and gains a
'method' argument. It defaults to the same repositories as
the other tools, those specified by getOption("repos").
BUG FIXES
o Configuring for Tcl/Tk makes use of ${TK_LIB_SPEC} ${TK_LIBS}
not ${TK_LIB_SPEC} ${TK_XLIBSW}, which is correct for
recent versions of Tk, but conceivably not for old
tkConfig.sh files.
o detach() was not recomputing the S4 methods for primitives
correctly.
o Methods package now has class "expression" partly fixed in basic
classes, so S4 classes can extend these (but "expression" is
pretty broken as a vector class in R).
o Collected warnings had messages with unneeded trailing space.
o S4 methods for primitive functions must be exported from
namespaces; this is now done automatically.
Note that is.primitive() is now in "base", not "methods".
o Package grid:
- Fixed bug in grid.text() when "rot" argument has length 0.
(reported by Emmanuel Paradis)
o .install_package_vignette_index() created an index even in an
empty 'doc' directory.
o The print() method for factors now escapes characters in the
levels in the same way as they are printed.
o str() removed any class from environment objects.
str() no longer interprets control characters in character
strings and factor levels; also no longer truncates factor
levels unless they are longer than 'nchar.max'.
Truncation of such long strings is now indicated ''outside''
the string.
str(<S4.object>) was misleading for the case of a single slot.
str() now also properly displays S4 class definitions (such as
returned by getClass().
o print.factor(quote=TRUE) was not quoting levels, causing
ambiguity when the levels contained spaces or quotes.
o R CMD check was confused by a trailing / on a package name.
o write.table() was writing incorrect column names if the data
frame contained any matrix-like columns.
o write.table() was not quoting row names for a 0-column x.
o t(x)'s default method now also preserves names(dimnames(x)) for
1D arrays 'x'.
o r <- a %*% b no longer produces names(dimnames(r)) == c("", "")
unless one of a or b has named dimnames.
o Some .Internal functions that were supposed to return invisibly
did not. This was behind PR#7397 and PR#7466.
o eval(expr, NULL, encl) now looks up variables in encl, as
eval(expr, list(), encl) always did
o Coercing as.data.frame(NULL) to a pairlist caused an error.
o p.adjust(p, ..) now correctly works when `p' contains NAs (or when
it is of length 0 or length 2 for method = "hommel").
o 'methods' initialization was calling a function intended for
.Call() with .C().
o optim() needed a check that the objective function returns a
value of length 1 (spotted by Ben Bolker).
o X11() was only scaling its fonts to pointsize if the dpi
was within 0.5 of 100dpi.
o X11() font selection was looking for any symbol font, and
sometimes got e.g. bold italic if the server has such a font.
o dpois(*, lambda=Inf) now returns 0 (or -Inf for log).
o Using pch="" gave a square (pch=0)! Now it is regarded as the
same as NA, which was also undocumented but omits the point.
o Base graphics now notices (ab)lines which have a zero
coordinate on log scale, and omits them. (PR#7559)
o stop() and warning() now accept NULL as they are documented
to do (although this seems of little use and is equivalent to "").
o weighted.mean() now checks the length of the weight vector w.
o getAnywhere() was confused by names with leading or trailing dots
(spotted by Robert McGehee)
o eval() was not handling values from return() correctly.
o par(omd) is now of the form c(x1, x2, y1, y2) to match the
documentation and for S-PLUS compatibility.
[Previously, par(omd) was of the form c(bottom, left, top, right)
like par(oma) and par(omi)]
o formatC() did not check its 'flag' argument, and could
segfault if it was incorrect. (PR#7686)
o Contrasts needed to be coerced to numeric (e.g. from integer)
inside model.matrix. (PR#7695)
o socketSelect() did not check for buffered input.
o Reads on a non-blocking socket with no available data were
not handled properly and could result in a segfault.
o The "aovlist" method for se.contrast() failed in some very
simple cases that were effectively not multistratum designs,
e.g. only one treatment occurring in only one stratum.
o pgamma() uses completely re-written algorithms, and should work
for all (even very extreme) arguments; this is based on Morten
Welinder's contribution related to PR#7307.
o dpois(10, 2e-308, log=TRUE) and similar cases gave -Inf.
o x <- 2^(0:1000); plot(x, x^.9, type="l", log="xy")# and
x <- 2^-(1070:170); plot(x, x^.9, type="l", log="xy")# now both work
o summary.lm() asked for a report on a reasonable occurrence, but
the check failed to take account of NAs.
o lm() was miscalculating 'df.residual' for empty models with a
matrix response.
o summary.lm() now behaves more sensibly for empty models.
o plot.window() was using the wrong sign when adjusting
xlim/ylim for positive 'asp' and a reversed axis.
o If malloc() fails when allocating a large object the allocator now
does a gc and tries the malloc() again.
o packageSlot() and getGroupMembers() are now exported from the
'methods' package as they should from documentation and the
Green Book.
o rhyper() was giving numbers slightly too small, due to a bug in the
original algorithm. (PR#7314)
o gsub() was sometimes incorrectly matching ^ inside a string,
e.g. gsub("^12", "x", "1212") was "xx".
o [g]sub(perl = TRUE) was giving random results for a 0-length
initial match. (PR#7742)
o [g]sub was ignoring most 0-length matches, including all initial
ones. Note that substitutions such as gsub("[[:space:]]*", "
", ...) now work as they do in 'sed' (whereas the effect was
previously the same as gsub("[[:space:]]+", " ", ...)).
(In part PR#7742)
o Promises are now evaluated when extracted from an environment
using '$' or '[[ ]]'.
o reshape(direction="wide") had some sorting problems when
guessing time points (PR#7669)
o par() set 'xaxp' before 'xlog' and 'yaxp' before 'ylog',
causing PR#831.
o The logic in tclRequire() to check the availability of a Tcl
package turned out to be fallible. It now uses a try()-and-see
mechanism instead.
o Opening a unz() connection on a non-existent file left a file
handle in use.
o "dist" objects of length 0 failed to print.
o INSTALL and the libR try harder to find a temporary directory
(since there might be one left over with the same PID).
o acf() could cause a segfault with some datasets. (PR#7771)
o tan(1+LARGEi) now gives 0+1i rather than 0+NaNi (PR#7781)
o summary(data.frame(mat = I(matrix(1:8, 4)))) does not go into
infinite recursion anymore.
o writeBin() performed byte-swapping incorrectly on complex
vectors, also swapping real and imaginary parts. (PR#7778)
o read.table() sometimes discarded as blank lines containing
only white space, even if sep=",".
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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