R 1.2.0 is released

Peter Dalgaard BSA p.dalgaard at biostat.ku.dk
Fri Dec 15 12:42:57 CET 2000

I've rolled up R-1.2.0.tgz a moment ago. This release has major
improvements in efficiency and memory handling. 

You can get it from




or wait for it to be mirrored at a CRAN site near you within a day or two.

There's also a version split in three for floppies.

	For the R Core Team,

	Peter D.

Here's the relevant part of the NEWS file:



    o	There is a new memory management system using a generational
	garbage collector.  This improves performance, sometimes
	marginally but sometimes by double or more.  The workspace is
	no longer statically sized and both the vector heap and the
	number of nodes can grow as needed.  (They can shrink again,
	but never below the initially allocated sizes.)	 See ?Memory
	for a longer description, including the new command-line
	options to manage the settings.

    o	values of `--min-nsize' up to 50M (2Gb on 64-bit Solaris) are

    o	A (preliminary) version of S4-like connections has been added,
	and most functions which take a "file" argument can now work
	with a connection as well as a file name.  For more details,
	see the chapter on Connections in the R Data Import/Export

    o	New command-line option `--no-restore-history' implied by

    o	Command-line option `--no-restore' is now `--no-restore-data'
	and `--no-restore' implies `--no-restore-*' (currently `data'
	and `history').

    o	The more recent GNU regex from grep-2.4.2 is used.  This uses
	locale-based ordering for ranges on platforms with strcoll.

    o	The print routines now escape " (as \") in a character string
	only when it is printed as a quoted string.  This makes
	print(, quote=FALSE) and cat() consistent.

    o	The standard methods for add1() and drop1() now attempt to cope
	with missing values by using a subset of the data that is
	`cleaned' by na.action for the maximal model under consideration.

    o	anova() for 3 or more lm objects now behaves compatibly	with S
	and anova.glmlist().  The old behaviour is still available by
	calling anovalist.lm() directly.

    o	anova() for multiple lm and glm objects no longer truncates the
	formula printed. There is much more extensive documentation 
	for anova() methods.

    o	New method as.data.frame.table() for converting the array-based
	representation of a contingency table to a data frame containing
	the classifying factors and the corresponding counts.

    o	New function assocplot() for producing Cohen-Friendly
	association plots.

    o	autoload() accepts lib.loc and other arguments to library()

    o	bxp() has new argument `frame.plot', as plot.default().

    o	contour() now has `axes' and `frame.plot' args.

    o	contrasts(, FALSE) now always returns an identity matrix,
	to make model.matrix compatible with S. This affects models
	such as lm(y ~ o - 1) where o is an ordered factor.

    o	`where' command added to debug().

    o	demo(dynload) (which used the superseded call_R interface)
	has been removed.

    o	Class "dendrogram" in package mva providing general support
	for tree-like structures (plotting, cutting, ...).

    o	dev.copy2eps() and dev2bitmap() preserve the aspect ratio of the
	copied device if just one of `width' and `height' is specified.

    o	dump() has new argument append, argument `fileout' has been
	renamed to `file' (for consistency with all other functions).

    o	edit.default() now checks for an unset `editor' argument, and
	terminates with an error if the editor cannot be run.

    o	The `mode' argument of exists() and get() is interpreted
	as mode(x) rather than typeof(x), following S.

    o	New functions file.access() and file.info() for information on
	files on the user's file systems.

    o	New convenience function file.copy().

    o	file.show() allows `pager' argument to be an R function, and
	consequently, the `pager' option can be an R function. 

    o	Formatting (and printing) of data.frames with complex objects is
	improved.  toString was added as a new function.

    o	format() has a new argument `justify' controlling the
	justification of character strings (and factors).

    o	Formula objects now have an environment and code manipulating
	them needs to take care to preserve it or set an appropriate

    o	New function fourfoldplot() for producing fourfold displays of
	2 by 2 by k contingency tables.

    o	gc() now reports the space allocated, not the space free,
	since the total space is now variable.

    o	New primitive gc.time() to report on time spent in garbage

    o	hclust() takes new argument `members' allowing dissimilarity
	matrices both for singletons (as until now) and clusters.

    o	help() has an additional `pager' argument which may be passed to
	file.show()  {useful for ESS fans}.

    o	There is now an R `Hershey' list object for Hershey vector font
	computations and documentation.

    o	hist() now returns a "histogram" object and calls the new
	function plot.histogram() for plotting.
	It now also allows character labels.

    o	if(*) now gives a more intelligible error message
	when "*" cannot be coerced to logical.

    o	inherits() is now an internal function and compatible with S.

    o	New function lag.plot() in package ts.

    o	legend() has a new argument pt.bg.

    o	The commands history can be loaded with loadhistory(), saved
	with savehistory() and displayed with history(), under Windows
	and under Unix using the readline or GNOME interfaces.

    o	mad() has new (logical) arguments "low" and "high" (the first 
	giving S compatibility).
    o	New function manova() and summary method.

    o	Function mantelhaen.test() in package ctest now can deal with
	general I x J x K tables.  In addition, in the 2 x 2 x K case,
	it can also perform an exact conditional test of independence,
	and gives confidence intervals for the common odds ratio.

    o	model.frame() now uses the environment of its formula argument,
	rather than the parent environment, to evaluate variables not
	found in the data argument. See help(formula).

    o	mosaicplot() can now also create extended mosaic plots, which
	visualize the residuals from a log-linear model using color and

    o	New utility function n2mfrow().

    o	nlm(check.analyticals = TRUE) now warns if the supplied
	gradient and/or hessian are of the wrong length.
    o	New function object.size() to give approximate memory allocation.

    o	optim() now checks the length of an analytical gradient at
	each evaluation.

    o	The L-BFGS-B method of optim() now support tracing, at several
	levels of detail.

     o	options(check.bounds = TRUE)  makes each vector extension
	by sub-assignment ("x[.] <- .") produce a warning.

   o	options(width) now admits to a limit (previously 200, now
	10000) and gives a more informative message if out of range
	(as it does now for digits and expressions).

    o	Function path.expand() to do tilde-expansion on file paths.
	This provides an interface to R_ExpandFileName, which is now
	a documented entry point.

    o	.Platform has new component "endian", useful for binary file

    o	plot.function() and curve() now take xlim as default for (from,to)
	if the former is specified.

    o	plot.hclust() allows arguments main, sub, etc, and has non-empty
	defaults for these.

    o	plot.ts(x,y) now allows to suppress labels and lines; 
	it is better documented.

    o	The postscript() driver now allows a user-specified family so,
	for example, one can use the same fonts in diagrams as in 
	running text.

    o	The postscript() driver allows its prolog to be changed (by an
	expert) via object .ps.prolog.

    o	prop.table() and margin.table() now work with an empty `margin'.

    o	Formerly deprecated function provide() is now defunct.

    o	New functions read.delim() and read.delim2() to make it
	easier to read delimited files as Windows programs tend to
	create (usually TAB separated).

    o	New readLines() function to read a file line-by-line.

    o	New functions reshapeLong() and reshapeWide() emulating Stata's
        reshape command. These are still labeled experimental and
        might be improved (or removed) in later versions.

    o	row.names() and row.names<-() are now generic functions which
	call rownames() as their default method and have methods for
	class "data.frame".

    o	New function Rprof() for profiling R expressions under Unix.
	Configure with `--enable-R-profiling' (on by default) to make
	this operational.

    o	save(, oldstyle=TRUE) has been withdrawn.

    o	scan() and read.table() have a new argument `fill' which can
	be set TRUE to allow reading files with unequal number of
	fields per line. (Programs like Excel have a habit of creating
	such files when exporting.)

    o	scan() and read.table() have a new argument `blank.lines.skip'
	to allow blank lines to be read.

    o	scan() now reads empty character fields as "" not "NA" unless
	"" is included in na.strings.

    o	smooth() in package eda has a better default (3RS3R instead of
	3RSR) and more arguments, e.g. `twiceit' for some S
	compatibility and kind = "3R" for running medians of 3.

    o	strsplit() has a new argument `extended' controlling whether to
	use extended (the default) or basic regular expressions for
    o	Sys.getenv() becomes the preferred name for getenv(), which is
	now deprecated.

    o	New functions Sys.getlocale() and Sys.setlocale() to query and
	set aspects of the locale of the R process, and
	Sys.localeconv() to find the default decimal point, etc.

    o	New function Sys.info() for platform, host and user information.

    o	New function Sys.putenv() to set environment variables.

    o	New function Sys.sleep() to suspend execution for a while.

    o	Date-time support functions with classes "POSIXct" and
	"POSIXlt" to represent dates/times (resolution 1 second) in
	the POSIX formats.  Functions include Sys.time(), as.POSIXct(),
	strftime(), strptime(),	 and methods for format, plot, c, ....
	There are conversion functions for objects from packages
	`date' and `chron'; unlike those packages these support
	functions know about time zones (if the OS does).

    o	tcltk library now has tkpager() which is designed to be used
	by file.show() and shows help pages etc. in separate text

    o	tcltk is now more careful about removing the objects
	representing widgets in the R workspace when the windows are
	destroyed (e.g. using window manager controls)	

    o	tcltk library has had several canvas functions implemented.
    o	tcltk now wraps callbacks to R in a try() construct - the
	nonlocal return from R's error handling could bring the Tk
	system into a strange state.  

    o	New demos for tcltk: tkfaq, tkfilefind, tkcanvas. 

    o	termplot() now has an `ask' argument.

    o	terms() creates objects which now inherit from class "formula",
	so for example as.formula(terms.object) needs to replaced by 

    o	traceback() is now printed un-quoted and labelled by the
	frame number.

    o	New argument `recursive' to unlink(). The default behaviour on
	Unix is now that of rm -f, not rm -rf.	unlink() is now
	compatible across platforms.

    o	New functions write.ftable() and read.ftable() for writing out
	and reading in flat contingency tables.

    o	write.table() now quotes factor columns if quote=TRUE, and has
	a new argument `qmethod' to control the escaping of
	embedded quotes in character or factor columns.

    o	New function xtabs() providing a formula interface to cross

    o	The R Data Import/Export Manual (`R-data.texi') has been added.

    o	The set of valid R names is now described (at last) in R-intro.

    o	The R Language Manual (`R-lang.texi') is now included and built
	in the same way as the other manuals.

    o   The R manuals (R-intro, R-exts, ...) are converted to HTML
        format (if the necessary texinfo tools are available) and
	linked into the top HTML help page.

    o	The header file `R.h' and those included from it are now usable
	with C++ code.

    o	New header file `R_ext/Boolean.h': Rboolean type with TRUE and
	FALSE enum constants.

    o	New header file `Rgraphics.h' to allow addons to use graphics

    o	Recommended include file `Rmath.h' replaces `R_ext/Mathlib.h'.

    o	Bessel, beta and gamma functions are now documented as part of
	the API.  Undocumented entry points are no longer in the
	header files, and some are no longer visible.

    o	Calloc & Realloc failures now give size information.

    o	DESCRIPTION file in installed packages has a new `Built:' field
	giving build information (R version, platform, date).

    o	Much improved support for C++ code in add-on packages under Unix.
	New configure/build variables SHLIB_CXXLD and SHLIB_CXXLDFLAGS
	for specifying the command and flags needed for building shared
	libraries containing objects from a C++ compiler.
	Configure tries to get these right in typical cases (GNU tools
	and/or common platforms).
	C++ source suffixes `.cpp' and `.C' are now recognized in
	addition to `.cc'.

    o	Configure/build variables MAINLD and MAINLDFLAGS are renamed to
	MAIN_LD and MAIN_LDFLAGS for consistency with other MAIN_* vars,
	similarly for SHLIBLD and SHLIBLDFLAGS.

    o	Configure/build variable FLIBS now only contains the Fortran 77
	intrinsic and run-time libraries needed for linking a Fortran 77
	program or shared library (as determined by configure).	 BLAS
	library detection was extended, with results saved to the Make
	variable BLAS_LIBS which is also available to add-on packages.

    o	R CMD build and check have been completely re-written in Perl.
	In addition to running examples, check now also checks the
	directory structure and control files, makes a temporary
	installation and runs LaTeX on the help pages.	Build has been
	reduced to cleaning, rewriting indices and creating tar files.

	The same files of Perl code are now also used under Windows.

    o	Add-ons for utilities like Perl or LaTeX have now a central
	place in $R_HOME/share. Migration of existing files might take
	a while, though.

    o	Preliminary support for building R as a shared library (`libR')
	under Unix.  Use configure with option `--enable-R-shlib' or do
	`make libR' in directory `src/main' to create the shared
	There is also a linker front-end `R CMD LINK' which is useful
	for creating executable programs linked against the R shared


    o	New "[.AsIs" function fixing PR#665.

    o	Effectively zero-length arrows() are omitted (rather than getting
	a system- and device-dependent arbitrary angle).

    o	barplot() passes "..." down to plot.window as documented.

    o	bxp(*) now obeys axes, xaxt, yaxt & ylim arguments (again?).

    o	contour(.., labcex = 0.6, .. , vfont = c("sans serif", "plain"), ..)
	now behaves as it has been documented, PR#740.

    o	D(.) is now more correctly documented, has second argument
	"name" instead of "namevec" (S compatibility), and gives a warning
	when name has not length 1.

    o	dbinom() and dpois() now use a the accurate algorithm of C.Loader;
	e.g., 1 - 2*sum(dbinom(0:999, 1999, 1/2)) is now zero instead of 1e-12.

    o	dbeta(), df(), dt(), dnbinom(), dgeom(), dgamma(),
	now all use the more accurate algorithms of dbinom() and dpois();
	More limits are computed correctly, e.g. dgeom(Inf,*), or
	dnbinom(*,*,p=0), and integer argument coercion is more consistent.
    o	dbeta(x, a,b) was giving NaN and Inf for large a and b.

    o	The math functions now (again!) return NaN (not NA)
	when the warning message says so (e.g. gamma(-1)).

    o	Paper sizes for "a4" and "legal" were interchanged in dev.print().

    o	Improved logic in the re-scaling of plots in dev.print().

    o	dev.print() and dev.copy2eps() now evaluate arguments as
	needed, so e.g. dev.print(file="junk.ps", horizontal=F) will
	work (previously =FALSE was needed).

    o	Now dweibull(0,1) == dexp(0) == 1 for consistency.

    o	Changing column modes from factor/character to numeric in
	edit.data.frame() (and fix() on data frames) is now allowed.

    o	gctorture() did return a value although documented not to, that of
	gcinfo.	 It now returns the previous setting of gctorture.

    o	glm() now follows lm() in dropping unused factor levels when fitting.

    o   hist() now labels y-axis Density rather than Relative Frequency
        if freq=FALSE. The `intensities' component of the result is
	now deprecated and `density' should be used instead. 

    o	hsv() truncation bug fixed (hopefully correctly this time...)

    o	library.dynam() no longer fails if the library appears more than
	once in lib.loc.

    o	lm.fit & lm.wfit (and hence lm) now give understandable error
	messages when there are 0 non-NA cases.

    o	match() does not always use "as.character()" anymore, fixes PR#741.

    o	Trimmed mean() and median() are no longer attempted for complex

    o	median() of empty vector is now NA.

    o	model.matrix() can now handle NAs in factors.

    o	model.matrix() now uses ":" not "." in labelling interaction
	terms, as terms() and the prototype do (PR#701).

    o	old.packages() now sorts version strings correctly by
	splitting at "." and "-".

    o	optim() has several new precautions against bugs, one of which was
	an infinite loop in the L-BFGS-B method if the derivatives
	were inaccurate (or if numerical derivatives were used and the
	problem was badly scaled).

    o	pairs() now obeys an "cex = " argument, and so does panel.smooth().

    o   pf() had a bug in the code handling large noncentrality
        parameters, going all the way back to the original Appl.Stat.
	algorithm (PR#752). This affected pbeta() as well.

    o	phantom(expr) in plotmath was used to calculate the bounding
	boxes, but the space was not actually used in typesetting the 
	expression (PR#622).

    o   Problem with subsetting and "..." arguments in plot.formula()

    o	plot.lm() has a better default for its `ask' argument.

    o	plot.new() does *NOT* allow an argument (`ask') anymore.
	This has not been working (since ~ R 0.49), is low-level and
	hence should not break anything.

    o	plot.stl() now uses correct time labels for tickmarks of x-axes.

    o	pnorm() is somewhat more accurate (SIXTEN=16; PR#699) and
	`infinitesimally faster' in some cases, thanks to James M. Rath.

    o	Failure to open a postscript() device now gives diagnostic warnings.

    o	Zero the widths of undefined chars in postscript().

    o	Make font metrics local to the device in postscript(), so
	that simultaneous instances of postscript/xfig/bitmap can use
	different values for `family'.

    o	postscript() no longer uses the initclip operator, which
	was against the EPSF specifications and broke inclusion of
	graphics in some documents.

    o	In postscript(), cleaned up the internals to fix some
	cases where it was unclear whether a variable was meant to set
	or track device status.

    o	In some cases, emitted postscript violated the PS Document
	Structuring Conventions since some settings were carried over from
	one page to the next. (Caused breakage when turning
	antialiasing on/off in "gv" for instance.)

    o	The DocumentMedia comment in postscript() output was wrong,
	and the font DSC comments have been changed to the preferred
	style for DSC 3.0.

    o	pretty(x <- c(2.8,3))[1] - x[1] is now 0; in general,
	p <- pretty(x) now again fulfills  p[1] <= x[] <= p[length(p)].

    o	print.dist() {mva} now passes "..." to print.default.

    o	print.noquote("ABC") now works.

    o	prompt(fn) uses fn's "source" attribute if it has one.

    o	In prop.test(), the conf.int. now contains the estimate,
	even when that is 0 or 1 (PR#714).

    o	qnorm(0) and qnorm(1) now give -/+ Inf (again!).

    o	qt(*, log = TRUE) has a somewhat extended working range.

    o	Specifying col.names in read.table() now overrides any header
	line in the data file.

    o	Bug caused rpois() to generate biased variables in some cases.

    o	scale(scale=TRUE) gave all NAs in any columns containing NAs.

    o	eda's smooth() now computes Tukey's endrule properly.

    o	smooth.spline()'s GCV method now uses a more accurate formula
	when there are repeated x points.

    o	stars() fix (for 0/NA columns) PR#739.
    o	data(state)'s  state.abb  has been corrected to use official
	2-letter abbrevations.

    o	strsplit() had two memory leaks.

    o	tcltk interface now has better string quoting and no longer breaks on
	strings with unbalanced braces

    o	tcltk callbacks used to include a "%..." argument on the call if the
	callback function had a "..." argument. This is no longer the case.

    o	t.test() allows an input vector of length 2.

    o	Method dispatch in primitive functions such as `c' only
	occurred if they were called by that name, and in particular
	not if used in lapply or called as .Primitive("c").  It now
	always occurs.

    o	Method dispatching now forces evaluation of promises, so
	autoloading works with methods.

    o	c(0.099999994, 0.2) prints as 0.1 0.2 not 0.10 0.20 after
	correcting the precision calculations.

    o	Internal function fprec was overflowing for numbers around

    o	[internal] .C("strsignif",*) doesn't use fixed size strings anymore
	(possible overflow).

    o	ff[i] <- r  now works for formula (and potentially other
	non-standard) objects ff.

    o	Errors in argument matching could cause crashes if error
	handler was used.

    o	NULL == ... now gives logical(0) instead of an error.
	This fixes a bug with e.g. apply(X,2,median, na.rm = TRUE) and
	all(NULL == NULL) is now TRUE.

    o	polylines with more than 64K pieces will now work on more X
	servers with the x11 device.

    o	R CMD Rd2dvi now again works with file names containing "_" or "$".

    o	R CMD Rdconv now handles .rd as input file extension correctly
        in all cases.

    o	make install could fail if there were no shared libraries to
	install (e.g. on vanilla Solaris).

    o	Rd's \describe{} constructs are converted better to text
	output, and \items of >=22 chars now work.

    o	Help aliases "(" and "{" now work, apart from as PDF hyperlinks.

    o	NA || x , NA && y (etc) do not give errors anymore, but work as
	the "|" and "&" operators and as documented (PR#749).

    o   Coercing lists to functions failed if argument list was empty.
        (PR#743). Also coercing functions to lists was wrong when the
	body was a single constant.

   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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