				Dear Emacs, please make this -*-Text-*- mode!
	**************************************************
	*						 *
	*	       1.5 SERIES NEWS			 *
	*						 *
	**************************************************


		CHANGES IN R VERSION 1.5.0


USER-VISIBLE CHANGES

    o	XDR support is now guaranteed to be available, so the default
	save format will always be XDR binary files, and it is safe to
	distribute data in that format.  (We are unaware of any
	platform that did not support XDR in recent versions of R.)

	gzfile() is guaranteed to be available, so the preferred
	method to distribute sizeable data objects is now via
	save(compress = TRUE).

    o	pie() replaces piechart() and defaults to using pastel colours.

    o	formatC has new arguments (see below) and formatC(*, d = <dig>)
	is no longer valid and must be written as formatC(*, digits = <dig>).

    o	Missingness of character strings is treated much more
	consistently, and the character string "NA" can be used as a
	non-missing value.

    o   summary.factor() now uses a stable sort, so the output will
	change where there are ties in the frequencies.


NEW FEATURES

    o   Changes in handing missing character strings:

        -  "NA" is no longer automatically coerced to a missing value
	   for a character string.  Use as.character(NA) where a missing
	   value is required, and test via is.na(x) not x == "NA".
	   String "NA" is still converted to missing by scan() and
	   read.table() unless `na.strings' is changed from the default.

        -  A missing character string is now printed as `NA' (no quotes)
	   amongst quoted character strings, and `<NA>' if amongst
	   unquoted character strings.

        -  axis() and text.default() omit missing values of their
	   `labels' argument (rather than plotting "NA").

        -  Missing character strings are treated as missing much more
	   consistently, e.g. in logical comparisons and in sorts.
	   identical() now differentiates "NA" from the missing string.


    o   Changes in package methods:

	-  New function validSlotNames().

	-  Classes can explicitly have a "data part", formally
	   represented as a .Data slot in the class definition, but
	   implemented consistently with informal structures.  While the
	   implementation is different, the user-level behavior largely
	   follows the discussion in "Programming with Data".

       -   A "next method" facility has been provided, via the function
	   callNextMethod().  This calls the method that would have been
	   selected if the currently active method didn't exist.  See
	   ?callNextMethod().  This is an extension to the API.

       -   Classes can have initialize methods, which will be called
	   when the function new() is used to create an object from the
	   class.  See ?initialize.  This is an extension to the API.

       -   The logic of setGeneric() has been clarified, simplifying
	   nonstandard generic functions and default methods.


    o	Changes in package tcltk:

        -  Now works with the GNOME user interface.

        -  Several new functions allow access to C level Tcl objects. 
	   These are implemented using a new `tclObj' class, and this
	   is now the class of the return value from .Tcl() and tkcmd().


    o	Changes in package ts:

	-  More emphasis on handling time series with missing values
	   where possible, for example in acf() and in the
	   ARIMA-fitting functions.

	-  New function arima() which will replace arima0() in due
           course.  Meanwhile, arima0() has been enhanced in several
           ways.  Missing values are accepted.  Parameter values can
           be initialized and can held fixed during fitting.  There is
           a new argument `method' giving the option to use
           conditional-sum-of-squares estimation.

	-  New function arima.sim().

	-  New datasets AirPassengers, Nile, UKgas and WWWusage,
	   and a expanded version of UKDriverDeaths (as a multiple
	   time series Seatbelts).

	-  New generic function tsdiag() and methods for arima and arima0,
	   to produce diagnostic plots.  Supersedes arima0.diag().

	-  New functions ARMAacf() and ARMAtoMA() to compute
           theoretical quantities for an ARMA process.

	-  New function acf2AR() to compute the AR process with a given
           autocorrelation function.

	-  New function StructTS() to fit structural time series, and
	   new generic function tsSmooth() for fixed-interval
	   state-space smoothing of such models.

	-  New function monthplot() (contributed by Duncan Murdoch).

	-  New functions decompose() and HoltWinters() (contributed by 
	   David Meyer) for classical seasonal decomposition and
	   exponentially-weighted forecasting.


    o	An extensible approach to safe prediction for models with e.g.
	poly(), bs() or ns() terms, using the new generic function
	makepredictcall().  Used by most model-fitting functions
	including lm() and glm().  See ?poly, ?cars and ?ns for
	examples.

    o   acosh(), asinh(), atanh() are guaranteed to be available.

    o   axis() now omits labels which are NA (but still draws the
	tick mark.

    o	Connections to bzip2-ed files via bzfile().

    o   chol() allows pivoting via new argument `pivot'.

    o	cmdscale() now takes rownames from a dist object `d' as well
	as from a matrix; it has new arguments `add' (as S) and `x.ret'.

    o   crossprod() handles the case of real matrices with y = x
	separately (by accepting y = NULL).  This gives a small
	performance gain (suggestion of Jonathan Rougier).

    o   deriv/deriv3() can now handle expressions involving pnorm and
	dnorm (with a single argument), as in S-PLUS.

    o	New function expm1() both in R and in C API, for accurate exp(x)-1;
	precision improvement in pexp() and pweibull() in some cases.
	(PR#1334-5)

    o	New function findInterval() {using new C entry point
	findInterval, see below}.

    o	formatDL() now also works if both items and descriptions are
	given in a suitable list or matrix.

    o	gzfile() is guaranteed to be available, and hence the
	`compress' option to save() and save.image().

    o	hist() now has a method for date-time objects.

    o	library() now checks the dependence on R version (if any) and
	warns if the package was built under a later version of R.

    o	library(help = PKG) now also returns the information about the
	package PKG.

    o	Added function logb(), same as log() but for S-PLUS
	compatibility (where log now has only one argument).

    o   New na.action function na.pass() passes through NAs unaltered.

    o   piechart() has been renamed to pie(), as piechart is a Trellis
	function for arrays of pie charts.  The default fill colours
	are now a set of pastel shades, rather than par("bg").

    o	plclust() in package mva, for more S-PLUS compatibility.

    o	poly() now works with more than one vector or a matrix as input,
	and has a predict method for objects created from a single
	vector.

    o	polyroot() now handles coefficient vectors with terminal
	zeroes (as in S).

    o	New prettyNum() function used in formatC() and format.default()
        which have new optional arguments `big.mark', `big.interval',
        `small.mark', `small.interval', and `decimal.mark'.

    o	print.coefmat() has a new argument 'eps.Pvalue' for determining
        when small P-values should be printed as  "< {...}".

    o   The recover() function has been moved to the base package.
        This is an interactive debugging function, usually a good
        choice for options(error=).  See ?recover.

    o	rep() has a new argument `each' for S-PLUS compatibility.
	The internal call is made available as rep.int(), again for
	help in porting code.

    o	New functions rowSums(), colSums(), rowMeans() and colMeans():
	versions of apply() optimized for these cases.

    o	rug() now has a "..." argument allowing its location to be specified.

    o	scan() can have NULL elements in `what', useful to save space
	when columns need to be discarded.

    o	New option by = "DSTday" for seq.POSIXt().

    o   Changes to sorting:

	-  sort(), sort.list() and order() have a new argument
	   `decreasing' to allow the order to be reversed whilst
	   still preserving ties.

	-  sort() has an option to use quicksort in some cases
	   (currently numeric vectors and increasing order).

	-  The default Shell sort is Sedgewick's variant, around 20%
           faster, and pre-screening for NAs speeds cases without any
	   NAs several-fold.

	-  sort.list() (and order with just one vector) is several
	   times faster for numeric, integer and logical vectors, and
	   faster for character vectors.

    o   New assignment forms of split(); new function unsplit().

    o	New sprintf() function for general C like formatting, from
	Jonathan Rougier.

    o	Argument `split' of summary.{aov,aovlist} is now implemented.

    o	summary.princomp() now has a separate print() method, and
	`digits' is now an argument to the print method and not to
	summary.princomp itself.

    o   An extended version of the trace() function is available,
        compatible with the function in S-PLUS.  Calls to R functions
        can be inserted on entry, on exit, and before any
        subexpressions. Calls to browser() and recover() are useful.
        See ?trace.

    o   New function TukeyHSD() for multiple comparisons in the results
	of aov().  (Formerly function Tukey in package Devore5 by
	Douglas Bates.)

    o	New read-only connections to files in zip files via unz().

    o	warning() has new argument `call.', like stop()'s.

    o	zip.file.extract() is no longer provisional and has an
	"internal" method available on all platforms.

    o	Methods for [, [<- and as.data.frame() for class "POSIXlt".

    o   Much improved printing of matrices and arrays of type "list".

    o	The "Knuth-TAOCP" option for random-number generation has been
	given an option of using the 2002 revision.  See ?RNG for the
	details: the R usage already protected against the
	reported `weakness'.

    o   min/max of integer(0) (or NULL) is now Inf/-Inf, not an
	extreme integer.


DEPRECATED & DEFUNCT

    o	.Alias, reshapeLong(), reshapeWide() are defunct.

    o	arima0.diag() (package ts) is deprecated: use tsdiag() instead.

    o	piechart() is deprecated; renamed to pie().


DOCUMENTATION CHANGES

    o	`Writing R Extensions' now has an example of calling R's
	random numbers from FORTRAN via C.

    o   R itself and all R manuals now have ISBN numbers, please use
        them when citing R or one of the manuals.


INSTALLATION CHANGES

    o	The configure script used when building R from source under Unix
	is now generated using Autoconf 2.50 or later, which has the
	following 'visible' consequences:

	- By default, configure no longer uses a cache file.  Use the
          command line option '--config-cache' (or '-C') to enable
          caching.

	- Key configuration variables such as 'CC' are now *precious*,
          implying that the variables

	  * no longer need to be exported to the environment and can and
            should be set as command line arguments;

	  * are kept in the cache even if not specified on the command
            line, and checked for consistency between two configure runs
            (provided that caching is used, see above);

	  * are kept during automatic reconfiguration as if having been
            passed as command line arguments, even if no cache is used.

	  See the variable output section of 'configure --help' for a
	  list of all these variables.

    o   Configure variable 'FC' is deprecated, and options '--with-g77',
	'--with-f77' and '--with-f2c' are defunct.  Use configure
	variable 'F77' to specify the FORTRAN 77 compiler, and 'F2C' to
	specify the FORTRAN-to-C compiler and/or that it should be used
	even if a FORTRAN 77 compiler is available.

    o	Non-standard directories containing libraries are specified
	using configure variable 'LDFLAGS' (not 'LIBS').


UTILITIES

    o	Sweave(), Stangle() and friends in package tools.  Sweave allows
	mixing LaTeX documentation and R code in a single source file:
	the R code can be replaced by its output (text, figures) to
	allow automatic report generation.  Sweave files found in
	package subdir 'inst/doc' are automatically tested by R CMD
	check and converted to PDF by R CMD build, see the section on
	package vignettes in the 'Writing R Extensions' manual.

    o	Rdconv can convert to the S4 '.sgml' format.

    o   R::Utils.pm masks some platform dependencies in perl code by
        providing global variables like R_OSTYPE or wrapper functions
        like R_runR().

    o   If a directory 'inst/doc' is present in the sources of a
        package, the HTML index of the installed package has a link to
        the respective subdirectory.

    o	R CMD check is more stringent: it now also fails on malformed
	'Depends' and 'Maintainer' fields in 'DESCRIPTION' files, and on
	unbalanced braces in Rd files.  It now also provides pointers to
	documentation for problems it reports.

    o	R CMD check, build and INSTALL produce outline-type output.

    o	QA functions in package 'tools' now return the results of their
	computations as objects with suitable print() methods.  By
	default, output	is only produced if a problem was found.

    o	New utility R CMD config to get the values of basic R configure
	variables, or the header and library flags necessary for linking
	against R.

    o   Rdindex and maketitle.pl require perl 5.005, as Text::Wrap::fill
	was only introduced at 5.004_05.


C-LEVEL FACILITIES

    o	All the double-precision BLAS routines are now available,
	and package writers are encouraged not to include their own
	(so enhanced ones will be used if requested at configuration).

    o	findInterval(xt[],n,x,...) gives the index (or interval number)
	of x in the sorted sequence xt[].  There's an
	F77_SUB(interv)(.) to be called from Fortran; this used to be
	part of predict.smooth.spline's underlying Fortran code.

    o	Substitutes for (v)snprintf will be used if the OS does not
	supply one, so tests for HAVE_(V)SNPRINTF are no longer needed.

    o	The DUP and NAOK arguments in a .C() call are not passed on
	to the native routine being invoked.  Any code that relied on
	the old behaviour will need to be modified.

    o	log1p is only provided in Rmath.h if it is not provided by the
	platform, in which case its name is not remapped, but a
	back-compatibility entry point Rf_log1p is provided.
	Applications using libRmath may need to be re-compiled.

    o	The methods used by optim() and integrate() have entry points in
	R_ext/Applic.h and have a more general interface documented in
	`Writing R Extensions'.

    o	The bessel_? entry points are now suitable to be called
	repeatedly from code loaded by .C().  (They did not free
	memory until .C() returned in earlier versions of R.)

    o	Server sockets on non-Windows platforms now set the SO_REUSEADDR
	socket option.  This allows a server to create simultanous
	connections to several clients.

    o	New quicksort sorting (for numeric no-NA data), accessible from
        C as R_qsort() etc and from Fortran as qsort4() and qsort3().

    o	Rinternals.h no longer includes fcntl.h, as this is not an
	ISO C header and cannot be guaranteed to exist.

    o	Fortran subroutines are more correctly declared as `extern void'
	in R_exts/Applic.h and R_exts/Linpack.h.


BUG FIXES

    o	The calculation of which axes to label on a persp() plot was
	incorrect in some cases.

    o	Insufficient information was being recorded in the display list
	for the identify() function.  In particular, the "plot="
	argument was ignored when replaying the display list. (PR#1157)

    o	The vertical alignment of mathematical annotations was wrong.
	When a vertical adjustment was not given, it was bottom-adjusting
	i.e,. it was treating adj=0 as adj=c(0, 0).  It now treats
	adj=0 as adj=c(0, 0.5) as for "normal" text. (PR#1302)

    o	the man page (doc/R.1) wasn't updated with the proper VERSION.

    o	smooth.spline() had a "df = 5" default which was never used and
	hence extraneous and misleading.

    o	read.fwf() was interpreting comment chars in its call to scan:
	replaced by a call to readlines(). (PR#1297/8)

    o	The default has been changed to scan(comment.char="") for
	consistency with earlier code (as in the previous item).

    o	bxp(*, notch.frac = f) now draws the median line correctly.

    o	Current versions of gs were rotating the output of
	bitmap(type = "pdfwrite") and when converting the output
	of postscript() to PDF; this has been circumvented by
	suppressing the %%Orientation comment for non-standard
	paper sizes.

    o	plot.ts(x, log = "y") works again when x has 0s, also for matrix x.

    o	add1(), drop1(), step() work again on glm objects with
	formulae with rhs's containing `.'.  (Broken by a `bug fix'
	(in reality an API change) in 1.2.1.)

    o	optim(method="BFGS") was not reporting reaching `maxit'
	iterations in the convergence component of the return value.

    o	aov() and model.tables() were failing on multistrata models with
	excessively long Error formula. (PR#1315)

    o	Transparent backgrounds on png() devices on Unix-alikes had
	been broken during the driver changes just prior to 1.4.0.
	(They worked correctly on Windows.)

    o	demo(is.things) didn't work properly when the methods package was
	attached.

    o	match(), unique() and duplicated() were not declaring all NaNs to be
	equal, yet not always distinguishing NA and NaN.  This was
	very rare except for data imported as binary numbers.

    o   The error handler recover() protects itself against errors in
        dump.frames and uses a new utility, limitedLabels, to generate
        names for the dump that don't inadvertently blow the limit on
        symbol length.  (TODO:  either fix dump.frames accordingly or
        remove the limit--say by truncating very long symbols?)

    o	se.contrasts() works more reliably with multistratum models,
	and its help page has an example.

    o	summary.lm() was not returning r.squared nor adj.r.squared for
	intercept-only models, but summary.lm.null() was returning
	r.squared but not adj.r.squared.  Now both are always
	returned.  Neither returned f.statistic, and that is now
	documented.

    o	Subsetting of matrices of mode list (or other non-atomic
	modes) was not implemented and gave incorrect results without
	warning. (PR#1329)
	Under some circumstances subsetting of a character matrix
	inserted NA in the wrong place.

    o   abs() was not being treated as member of the Math group
	generic function, so e.g. its method for data frames was not
	being used.

    o	set.seed(seed, "default") was not using the `seed' value (only
	for kind = "default").

    o	logLik.lm() now uses  "df = p + 1" again (`+ sigma'!).

    o	logLik.glm() was incorrect for families with estimated dispersion.

    o	Added strptime() workaround for those platforms (such as
	Solaris) that returned missing components as 0.  Missing
	days are now detected, but missing years will still
	be interpreted as 1900 on such platforms.

    o   Inheritance in formal classes (the methods package) works
        breadth-first as intuition would expect.

    o	The new() function in package `methods' works better (maybe even
        correctly?) for the various combinations of super-classes and
        prototypes that can be supplied as unnamed arguments.

    o	Internal code allowed one more connection to be allocated than
	the table size, leading to segfaults. (PR#1333)

    o	If a user asks to open a connection when it is created and
	it cannot be opened, the connection is destroyed before returning
	from the creation call.  (related to PR#1333)

    o	Sys.putenv() was not using permanent storage. (PR#1371)

    o	La.svd() was not coercing integer matrices. (PR#1363)

    o	deriv(3) now reports correctly the function it cannot find
	the derivatives table.

    o   The GNOME user interface was over-enthusiastic about setting
        locale information.  Now only LC_CTYPE, LC_COLLATE and LC_TIME
        are determined by the user's environment variables (PR#1321)

    o   In X11, locator() would sound the bell even if "xset b off"
        had been set.

    o	merge() could be confused by inconsistent use of as.character()
	giving leading spaces.

    o   [pqr]binom() no longer silently round the `size' argument,
	but return NaN (as dbinom() does). (PR#1377)

    o	Fixed socket writing code to block until all data is written.
	Fixed socket reading code to properly handle long reads and reads
	with part of the data in the connection buffer.

    o	Allow sockets to be opened in binary mode with both open="ab" and
	open="a+b".

    o	levels<-.factor() was using incorrectly list values longer than
	the number of levels (PR#1394), and incorrectly documented
	that a character value could not be longer than the existing
	levels.

    o   The pdf() device was running out of objects before the
	documented 500 page limit.  Now there is no limit.

    o   legend() did not deal correctly with `angle' arguments. (PR#1404)

    o   sum() tried to give an integer result for integer arguments,
	but (PR#1408)
	- this was not documented
	- it sometimes warned on overflow, sometimes not
	- it was order-dependent for a mixture of integer and numeric args.

    o	mean() gave (numeric) NA if integer overflow occurred in sum(),
	but now always works internally with numeric (or complex) numbers.

    o	sort.list() and order() were treating NA_STRING as "NA".

    o	sort.list(na.last = NA) was not implemented.

    o	seq.default() was returning only one element for a relative
	range of less than about 1e-8, which was excessively conservative.
	(PR#1416)

    o	tsp(x) <- NULL  now also works after library(methods).

    o	persp(shade=) was not working correctly with the default
	col=NULL if this was transparent. (PR#1419)

    o	min/max(complex(0)) was returning a random value.

    o   range() gave c(1, 1).

    o	range(numeric(0)) is now c(Inf, -Inf), as it was documented to be.

    o   print.ts() was occasionally making rounding errors in the labels
	for multiple calendar time series.

    o   Rdconv was not handling nested \describe{} constructs when
	converting to HTML (PR#1257) and not fixing up mal-formed
	\item fields in \describe{} when converting to text (PR#1330).

    o   filled.contour() was not checking consistency of x, y, z.
	(PR#1432)

    o   persp.default() no longer crashes with non-character labels.
	(PR#1431)

    o   fft() gave incorrect answers for input sizes 392, 588, 968, 980 ....
	(PR#1429)

    o   det(method = "qr") gave incorrect results for numerically
	singular matrices. (PR#1244)

    o   barplot() now allows the user to control `xpd'. (PR#1088, 1398)

    o   library() (with no arguments) no longer fails on empty TITLE files.

    o   glm() was failing if both offset() and start were specified. (PR#1421)

    o	glm() might have gotten confused if both step-shortening and
	pivoting had occurred (PR#1331).  Step-halving to avoid the
	boundary of feasible values was not working.

    o   Internal representation of logical values was not being
	treated consistently. (Related to PR#1439)

    o   The c() function sometimes inserted garbage in the name vector
        for some types of objects, e.g.  names(c(ls, a=1)).

    o   Fixed bug in `$' that could cause mutations on assignment (PR#1450).

    o   Some X servers displayed random bytes in the window title of
	graphics windows (PR#1451)

    o   The X11 data editor would segfault if closed with window manager
        controls (PR#1453)

    o	Interrupt of Sys.sleep() on UNIX no longer causes subsequent
	Sys.sleep() calls to segfault due to infinite recusion.

    o   Eliminated a race condition that could cause segfaults when a SIGINT
	was received while handling an earlier SIGINT.

    o   rect(lty = "blank") was incorrectly drawing with a dashed line.

    o   type.convert() was not reporting incorrectly formatting complex 
	inputs. (PR#1477)

    o   readChar() was not resetting vmax, so causing memory build-up.
	(PR#1483)



	**************************************************
	*						 *
	*	       1.4 SERIES NEWS			 *
	*						 *
	**************************************************


		CHANGES IN R VERSION 1.4.1


BUG FIXES

    o	scan(multi.line = FALSE) now always gives an immediate error
	message if a line is incomplete. (As requested in PR#1210)

    o	read.table() is no longer very slow in processing comments:
	moved to C code and fewer lines checked.

    o	type.convert() could give stack imbalance warnings if used
	with as.is = TRUE.

    o	predict.mlm ignored newdata (PR#1226) and also offsets.

    o	demo(tkttest) was inadvertently changed in 1.4.0 so that it would
	evaluate the requested test, but not display the result.

    o	stars(scale = TRUE) (the default) now works as documented (and
	as S does).  Previously it only scaled the maximum to 1. (PR#1230)

    o	d0 <- data.frame(a = 0); data.matrix(d0[0, 0]) and
	data.matrix(d0[, 0]) now work.

    o	plot(multiple time series, plot.type = "single") was computing
	`ylim' from the first series only.

    o	plot.acf() has a new `xpd = par("xpd")' argument which by default
	*does* clipping (of the horizontal lines) as desired (xpd = NA was
	used before, erronously in most cases).

    o	predict(smooth.spline(.), deriv = 1) now works.

    o	identify() failed when x is a structure/matrix. (PR#1238)

    o	getMethod() returns NULL when optional=TRUE as promised in the
	documentation.

    o	setMethod() allows "..." to be one of the arguments omitted in
	the method definition (but so far no check for ... being missing)

    o	Allow round() to work again on very large numbers (introduced
	in fixing PR#1138). (PR#1254)

    o	Rinternals.h is now accepted by a C++ compiler.

    o	type.convert() was failing to detect integer overflow.

    o	piechart() was defaulting to foreground colour (black) fills
	rather than background (as used in 1.3.1 and earlier).	Now
	background is used, but be aware that as from 1.4.0 this may
	be transparent.

    o	La.eigen(*, only.values=TRUE) does not segfault anymore in one
	branch (PR#1262).

    o	cut() now produces correct default labels even when
	include.lowest = TRUE (PR#1263).

    o	reformulate() works properly with a response.

    o	cmdscale(*, k = 1) now works properly.

    o	Options by = "month" and "year" to seq.POSIXt() will always
	take account of changes to/from daylight savings time: this
	was not working on some platforms.

    o	glm.fit.null() now accepts all the arguments of glm.fit() (it
	could be called from glm.fit with arguments it did not
	accept), and is now documented.

    o	cov.wt(cbind(1), cor = TRUE) now works.

    o	predict(glm.object, se.fit = TRUE) was failing if the fit
	involved an offset.

    o	detach() on package:base would crash R. (PR#1271)

    o	print or summary on a manova() object with no terms, no names on
	the response and intercept = FALSE (which is not sensible)
	would give an error.

    o	seek() on file connections was ignoring the `origin' argument.

    o	Fixed new environment handling in library() to avoid forcing
	promises created by delay()

    o	arima0() could leak memory: now released via on.exit().

    o	qr.coef(qr,*) now keeps the names of qr$qr.

    o	read.00Index() no longer fails on data indexes not generated by
	Rdindex (PR#1274).


		CHANGES IN R VERSION 1.4.0


USER-VISIBLE CHANGES

    [This is a new section to highlight changes in behaviour, which
    may be given in more detail in the following sections.
    Many bug fixes are also user-visible changes.]

    o	The default save format has been changed, so saved workspaces
	and objects cannot (by default) be read in earlier versions of R.

    o	The number of bins selected by default in a histogram uses
	the correct version of Sturges' formula and will usually be
	one larger.

    o	data.frame() no longer converts logical arguments to factors
	(following S4 rather than S3).

    o	read.table() has new arguments `nrows' and `colClasses'.  If the
	latter is NA (the default), conversion is attempted to
	logical, integer, numeric or complex, not just to numeric.

    o	model.matrix() treats logical variables as a factors with
	levels c(FALSE, TRUE) (rather than 0-1 valued numerical
	variables).  This makes R compatible with all S versions.

    o	Transparency is now supported on most graphics devices.
	This means that using par("bg"), for example in legend(), will
	by default give a transparent rather than opaque background.

    o	[dpqr]gamma now has third argument `rate' for S-compatibility
	(and for compatibility with exponentials).  Calls which use
	positional matching may need to be altered.

    o	The meaning of spar = 0 in smooth.spline() has changed.

    o	substring() and substring()<- do nothing silently on a
	character vector of length 0, rather than generating an
	error.	This is consistent with other functions and with S.

    o	For compatibility with S4, any arithmetic operation using a
	zero-length vector has a zero-length result.  (This was
	already true for logical operations, which were compatible
	with S4 rather than S3.)

    o	undoc() and codoc() have been moved to the new package `tools'.

    o	The name of the site profile now defaults to
	`R_HOME/etc/Rprofile.site'.

    o	The startup process for setting environment variables now first
	searches for a site environment file (given by the environment
	variable `R_ENVIRON' if set or `R_HOME/etc/Renviron.site' if
	not), *and* then for a user `.Renviron' file in the current or
	the user's home directory.

    o	Former stars(*, colors = v) must now be stars(*, col.segments = v).

    o	The default methods for La.svd and La.eigen have changed and
	so there may be sign changes in singular/eigen vectors,
	including in cancor, cmdscale, factanal, princomp and varimax.


NEW FEATURES

    o	Transparency is now supported on most graphics devices.
	Internally colors include an alpha channel for opacity, but at
	present there is only visible support for transparent/opaque.
	The new color "transparent" (or NA or "NA") is transparent,
	and is the default background color for most devices.  Those
	devices (postscript, XFig, PDF, Windows metafile and printer)
	that previously treated bg = "white" as transparent now have
	"transparent" as the default and will actually print "white".
	(NB: you may have bg = "white" saved in .Postscript.options in
	your workspace.)

    o	A package `methods' has been added, containing formal classes
	and methods ("S4" methods), implementing the description in
	the book "Programming with Data".  See "?Methods" and the
	references there for more information.

	- In support of this, the "@" operator has been added to the
	  grammar.

	- Method dispatch for formal methods (the standardGeneric
	  function), is now a primitive. Aside from efficiency issues,
	  this allows S3-style generics to also have formal methods
	  (not really recommended in the long run, but it should at
	  least work).	The C-level dispatch is now implemented for
	  primitives that use either DispatchGroup or DispatchOrEval
	  internally.

	- A version of the function "plot" in the methods package has
	  arguments "x" and "y", to allow methods for either or both.
	  See "?setMethod" for examples of such methods.

	- The methods package now uses C-level code (from within
	  DispatchOrEval) to dispatch any methods defined for
	  primitive functions.	As with S3-style methods, methods can
	  only be defined if the first argument satisfies is.object(x)
	  (not strictly required for formal methods, but imposed for
	  now for simplicity and efficiency).

    o	Changes to the tcltk package:

	- New interface for accessing Tcl variables, effectively
	  making the R representations lexically scoped. The old form
	  is being deprecated.

	- Callbacks can now be expressions, with slightly unorthodox
	  semantics. In particular this allows bindings to contain
	  "break" expressions (this is necessary to bind code to
	  e.g. Alt-x without having the key combination also insert an
	  "x" in a text widget.)

	- A bunch of file handling and dialog functions (previously
	  only available via tkcmd) have been added

    o	The "?" operator is now an actual function.  It can be used
	(as always) as a unary operator (?plot) and the grammar now
	allows it as a binary operator, planned to allow
	differentiating documentation on the same name but different
	type (class?matrix, for example).  So far, no such
	documentation exists.

    o	New methods AIC.default() and logLik.glm(), also fixing
	AIC(<glm obj>).

    o	axis.POSIXct() allows the label date/times to be specified
	via the new `at' argument.

    o	arrows() now allows length = 0 (and draws no arrowheads).

    o	Modifications to the access functions for more consistency with S:
	arguments `name', `pos' and `where' are more flexible in
	assign(), exists(), get(), ls(), objects(), remove() and rm().

    o	Three new primitive functions have been added to base:
	dataClass(), objWithClass(), and as.environment().  The first two
	are support routines for class() and class<-() in package
	methods.  The third replaces pos.to.env() in the functions get(),
	exists(), and friends.

    o	barplot() now respects an inline `cex.axis' argument and has a
	separate `cex.names' argument so names and the numeric axis
	labels can be scaled separately.  Also, graphics parameters
	intended for axis() such as `las' can now be used.

    o	Shading by lines added to functions barplot(), hist(),
	legend(), piechart(), polygon() and rect().

    o	bxp() has a show.names argument allowing labels on a single
	boxplot; it and hence boxplot() now makes use of pch, cex, and bg
	for outlier points().

	bxp() and boxplot() also have an argument `outline' to suppress
	outlier drawing {S-PLUS compatibly}.

    o	New capabilities() options "GNOME" and "IEEE754".

    o	New function casefold(), a wrapper for tolower/toupper
	provided for compatibility with S-PLUS.

    o	contour() is now generic.

    o	cor.test() in package ctest now also gives an asymptotic
	confidence interval for the Pearson product moment correlation
	coefficient.

    o	data(), demo() and library() now also return the information
	about available data sets, demos or packages.  Similarly,
	help.search() returns its results.

    o	density() allows `bw' or `width' to specify a rule to choose the
	bandwidth, and rules "nrd0" (the previous default), "nrd",
	"ucv", "bcv", "SJ-ste" and "SJ-dpi" are supplied (based on
	functions in package MASS).

    o	df.residual() now has a default method, used for classes
	"lm" and "glm".

    o	New argument `cacheOK' to download.file() to request cache
	flushing.

	All methods for download.file() do tilde-expansion on the path
	name.

	The internal download.file() etc now allow URLs of the form
	ftp://user@foo.bar/ and ftp://user:pass@foo.bar/

    o	duplicated() and unique() are now generic functions with
	methods for data frames (as well as atomic vectors).

    o	factanal() and princomp() use napredict() on their scores, so
	na.action = na.exclude is supported.

    o	Function getNativeSymbolInfo() returns details about a native
	routine, potentially including its address, the library in
	which it is located, the interface by which it can be called
	and the number of parameters.

    o	Functions such as help() which perform library or package index
	searches now use NULL as default for their `lib.loc' argument so
	that missingness can be propagated more easily.	 The default
	corresponds to all currently known libraries as before.

    o	Added function file.rename().

    o	hist.default() allows `breaks' to specify a rule to choose the
	number of classes, and rules "Sturges" (the previous default),
	"Scott" and "FD" (Freedman-Diaconis) are supplied (based on
	package MASS).

    o	Function identical(), a fast and reliable way to test for exact
	equality of two objects.

    o	New generic function is.na<-(), from S4.  This is by default
	equivalent to x[value] <- NA but may differ, e.g. for factors
	where "NA" is a level.

    o	is.xxx reached through do_is are now generic.

    o	La.eigen() and La.svd() have new default methods to use later
	(and often much faster) LAPACK routines.  The difference
	is most noticeable on systems with optimized BLAS libraries.

    o	length() is now generic.

    o	New function .libPaths() for getting or setting the paths to the
	library trees R knows about.  This is still stored in .lib.loc,
	which however should no longer be accessed directly.

    o	Using lm/glm/... with `data' a matrix rather than a data frame
	now gives a specific error message.

    o	loess(), lqs(), nls() and ppr() use the standard NA-handling
	and so support na.action = na.exclude.

    o	mahalanobis() now has a `tol' argument to be passed to solve().

    o	mean() has `data frame' method applying mean column-by-column.
	When applied to non-numeric data mean() now returns NA rather
	than a confusing error message (for compatibility with S4).
	Logicals are still coerced to numeric.

    o	The formula interface to mosaicplot() now allows a contingency
	table as data argument.

    o	new.env() is now internal and allows you to set hashing. Also,
	parent.env() and parent.env<-() are included to provide direct
	access to setting and retrieving environments.

    o	Function nsl() to look up IP addresses of hosts: intended as
	a way to test for internet connectivity.

    o	Ops(), cbind(), diff() and na.omit() methods for time series
	objects moved from package ts to package base.

    o	New option `download.file.method' can be used to set the
	default method for download.file() and functions which use it
	such as update.packages().

    o	order() and sort.list() now implement na.last = FALSE, NA.

    o	Started work on new package management system: packageStatus()
	and friends.

    o	page() has a new `method' argument allowing `method = print'.

    o	png(), jpeg() and bmp() devices now have a `bg' argument to
	set the background color: useful to set "transparent" on png().

    o	Changes to the postscript() device:

	- The symbol font can now be set on a postscript() device, and
	  support has been added for using Computer Modern type-1
	  fonts (including for symbols). (Contributed by Brian D'Urso.)

	- There is now support for URW font families: this will give
	  access to more characters and more appropriate metrics on
	  PostScript devices using URW fonts (such as ghostscript).

	- %%IncludeResource comments have been added to the output.
	  (Contributed by Brian D'Urso.)

    o	predict.ppr() now predicts on `newdata' containing NAs.

    o	princomp() now has a formula interface.

    o	readChar() now returns what is available if fewer characters
	than requested are on the file.

    o	readline() allows up to 256 chars for the prompt.

    o	read.table(), scan() and count.fields() have a new argument
	`comment.char', default `#', that can be used to start
	comments on a line.

    o	New function reg.finalizer() to provide R interface to
	finalization.

    o	reshape() extends reshapeLong, reshapeWide, which are deprecated.

    o	rle() now returns a classed object, has a print method and
	an inverse.

    o	Changes to save() and friends:

	- save() now takes an envir argument for specifying where
	  items to be saved are to be found.

	- A new default format for saved workspaces has been
	  introduced.  This format provides support for some new
	  internal data types, produces smaller save files when saving
	  code, and provides a basis for a more flexible serialization
	  mechanism.

	- Modified `save' internals to improve performance when saving
	  large collections of code.

	- save() and save.image() now take a `version' argument to
	  specify the workspace file-format version to use.  The
	  version used from R 0.99.0 to 1.3.1 is version 1.  The new
	  default format is version 2.	load() can read a version 2
	  saved workspace if it is compressed.

	- save() and save.image() now take a `compress' argument to
	  specify that the saved image should be written using the zlib
	  compression facilities.

	- save.image() now takes an argument `ascii'.

	- save.image() now takes an argument `safe'.  If TRUE, the
	  default, a temporary file is used for creating the saved
	  workspace.  The temporary file is renamed if the save
	  succeeds.  This preserves an existing workspace if the save
	  fails, but at the cost of using extra disk space during the
	  save.

	- save.image() default arguments can be specified in the
	  `save.image.defaults' option.	 These specifications are used
	  when save.image() is called from q() or GUI analogs.


    o	scan() allows unlimited (by R) lengths of input lines, instead
	of a limit of 8190 chars.

    o	smooth.spline() has a new `control.spar' argument and returns
	`lambda' besides `spar'.  spar <= 0 is now valid and allows
	to go more closely towards interpolation (lambda -> 0) than before.
	This also fixes smooth.spline() behavior for "df ~= n - 2". Better
	error messages in several situations.

	Note that spar = 0 is no longer the default and no longer entails
	cross-validation.

    o	stars() has been enhanced; new `mar' argument uses smaller
	mar(gins) by default; further `nrow and `ncol' as S-PLUS,
	`frame.plot', `flip.labels', `lty' and explicit `main', `sub',
	`xlab' and `ylab'.  Note that `colors' has been replaced by
	`col.segments' and there's a new `col.stars'.

	stars() now returns the locations invisibly.

    o	step() is now closer to stepAIC() and so handles a wider range
	of objects (but stepAIC [in MASS] is still more powerful).

    o	symbols() now has automatic xlab and ylab and a main argument
	which eliminates an incorrect warning.	It better checks wrongly
	scaled arguments.

    o	Sys.setlocale() now issues a warning if it fails.

    o	An enhanced function type.convert() is now a documented
	function, rather than just internal to read.table().

    o	warning() allows multiple arguments, following S4's style.

    o	New function with() for evaluating expressions in environments
	constructed from data.

    o	Unix x11() devices can now have a canvas color set, which can
	help to distinguish plotting "white" from plotting
	"transparent".

    o	On Unix, X11(), png() and jpeg() now give informative warnings
	if they fail to open the device.


    o	The startup processing now interprets escapes in the values of
	environment variables set in R_HOME/etc/Renviron in a similar
	way to most shells.

    o	The operator "=" is now allowed as an assignment
	operator in the grammar, for consistency with other languages,
	including recent versions of S-PLUS.  Assignments with "=" are
	basically allowed only at top-level and in braced or
	parenthesized expressions, to make famous errors such as
	"if(x=0) 1 else 2" illegal in the grammar.
	(There is a plan to gradually eliminate the underscore as an
	assignment in future versions of R.)

    o	Finalizers can be registered to be run on system exit for both
	reachable and unreachable objects.

    o	integer addition, subtraction, and multiplication now return NA's
	on overflow and issue a warning.

    o	Printing factors with both level "NA" and missing values
	uses `<NA>' for the missing values to distinguish them.

    o	Added an experimental interface for locking environments and
	individual bindings.  Also added support for "active bindings"
	that link a variable to a function (useful for example for linking
	an R variable to an internal C global).

    o	GNOME interface now has separate colours for input and output
	text (like the windows GUI). These can be modified via the
	properties dialogue.

    o	Output from the GNOME console is block buffered for increased
	speed

    o	The GNOME console inherits standard emacs-style keyboard
	shortcuts from the GtkText widget for cursor motion, editing
	and selection.	These have been modified to allow for the prompt
	at the beginning of the command line.

    o	One can register R functions and C routines to be called at the
	end of the successful evaluation of each top-level expression,
	for example to perform auto-saves, update displays, etc. See
	addTaskCallback() and taskCallbackManager(). See
	http://developer.r-project.org/TaskHandlers.pdf.


DEPRECATED & DEFUNCT

    o	.Alias has been removed from all R sources and deprecated.

    o	reshapeLong(), reshapeWide() are deprecated in favour of reshape().

    o	Previously deprecated functions read.table.url(), scan.url(),
	source.url(), httpclient() and parse.dcf() are defunct.
	Method "socket" for download.file() no longer exists.


DOCUMENTATION CHANGES

    o	`Writing R Extensions' has a new chapter on generic/method
	functions.


UTILITIES

    o	New package `tools' for package development and administration
	tools, containing the QA tools checkFF(), codoc() and undoc()
	previously in package base, as well as the following new ones:

	-  checkAssignFuns() for checking whether the final argument of
	   assignment functions in a package is named `value'.

	-  checkDocArgs() for checking whether all arguments shown in
	   \usage of Rd files are documented in the corresponding
	   \arguments.

	-  checkMethods() for checking whether all methods defined in a
	   package have all arguments of their generic.

	-  checkTnF() for finding expressions containing the symbols `T'
	   and `F'.

    o	R CMD Rd2dvi has more convenient defaults for its output file.

    o	R CMD check now also fully checks the Depends field in the
	package DESCRIPTION file.  It also tests for syntax errors in
	the R code, whether all methods in the code have all arguments
	of the corresponding generic, for arguments shown in \usage but
	not documented in \arguments, and whether assignment functions
	have their final argument named `value'.


C-LEVEL FACILITIES

    o	arraySubscript and vectorSubscript are now available to package
	users.	All "array-like" packages can use a standard method for
	calculating subscripts.

    o	The C routine type2symbol, similar to type2str, returns a symbol
	corresponding to the type supplied as an argument.

    o	The macro SHLIB_EXT now includes `.', e.g. ".so" or ".dll",
	since the Mac uses "Lib" without a `.'.

    o	New Fortran entry points rwarn() and rexit() for warnings and
	error exits from compiled Fortran code.

    o	A new serialization mechanism is available that can be used to
	serialize R objects to connections or to strings.  This
	mechanism is used for the version 2 save format.  For now,
	only an internal C interface is available.

    o	R_tryEval() added for evaluating expressions from C code with
	errors handled but guaranteed to return to the calling C
	routine. This is used in embedding R in other applications and
	languages.

    o	Support for attach()'ing user-defined tables of variables
	is available and accessed via the RObjectTables package
	currently at http://www.omegahat.org/RObjectTables.


BUG FIXES

    o	Fixed share/perl/massage-examples.pl to detect instances of
	par() at the very start of a line.

    o	Fixed Pearson residuals for glms with non-canonical
	link.(PR#1123). Fixed them again for weights (PR#1175).

    o	Fixed an inconsistency in the evaluation context for on.exit
	expressions between explicit calls to `return' and falling off
	the end returns.

    o	The code in model.matrix.default() handling contrasts was
	assuming a response was present, and so without a response was
	failing to record the contrasts for the first variable if it
	was a factor.

    o	diffinv() could get the time base wrong in some cases.

    o	file.append() was opening all files in text mode: mattered
	on Windows and classic Macintosh. (PR#1085)

    o	f[] <- g  now works for factor f.

    o	substr<-() was misbehaving if the replacement was too short.

    o	The version of `packages.html' generated when building R or
	installing packages had an incorrect link to the style sheet.
	The version used by help.start() was correct. (PR#1090)

    o	rowsum() now gives character (not factor codes) as rownames.
	(PR#1092)

    o	plot.POSIX[cl]t now respect the `xaxt' parameter.

    o	It is now possible to predict from an intercept-only model:
	previously model.matrix.default() objected to a 0-column
	model frame.

    o	c.POSIXct was not setting the right classes in 1.3.x.

    o	cor(*, use = "all.obs") <= 1 is now guaranteed which ensures
	that sqrt(1 - r^2) is always ok in cor.test(). (PR#1099)

    o	anova.glm() had a missing drop=FALSE and so failed for some
	intercept-less models.

    o	predict.arima0() now accepts vector as well as matrix
	`newxreg' arguments.

    o	cbind(d,f) now works for 0-column dataframes. This fixes PR#1102.

    o	plot(ts(0:99), log = "y") now works

    o	method "gnudoit" of bug.report() was incorrectly documented as
	"gnuclient" (PR#1108)

    o	saving with ascii=TRUE mangled backslashes. (PR#1115)

    o	frac(,) {and others} now adds a gap appropriately. (PR#1101)

    o	logLik.lm() now uses the correct "df" (nlme legacy code).

    o	closeAllConnections() works again, and closes all sink() diversions.

    o	sink(type="message") works again.

    o	sink.number was (accidentally) returning the result invisibly.

    o	as.POSIXct("NA") (or ..lt) now work; hence, merge(*, all=TRUE) now
	works with dataframes containing POSIXt date columns.

    o	integer(2^30+1) and similar ones do not segfault anymore but duly
	report allocation errors.

    o	seq(0, 0, 1) now works (PR#1133).

    o	reshapeWide() got it wrong if the "i" factor was not sorted (the
	function is now deprecated since reshape() is there, but the bug
	still needed fixing...)

    o	PR#757 was fixed incorrectly, causing improper subsetting of
	pch etc. in plot.formula().

    o	library() no longer removes environments of functions that are
	not defined in the top-level package scope.  Also, packages
	loaded by require() when sourcing package code are now visible
	in the remaining source evaluations.

    o	names(d) <- v  now works (again) for "dist" objects d. (PR#1129)

    o	Workarounds for problems with incompletely specified date-times
	in strptime() which were seen only on glibc-based systems
	(PR#1155).

    o	promax() was returning the wrong rotation matrix. (PR#1146)

    o	The [pqr]signrank and [pqr]wilcox functions failed to check that
	memory has been allocated (PR#1149), and had (often large)
	memory leaks if interrupted.  They now can be interrupted on
	Windows and MacOS and don't leak memory.

    o	range(numeric(0)) is now c(NA, NA) not NA.

    o	round(x, digits) for digits <= 0 always gives an integral
	answer.	 Previously it might not due to rounding errors in
	fround. (PR#1138/9)

    o	Several memory leaks on interrupting functions have been
	circumvented.  Functions lqs() and mve() can now be
	interrupted on Windows and MacOS.

    o	image() was finding incorrect breakpoints from
	irregularly-spaced midpoints. (PR#1160)

    o	Use fuzz in the 2-sample Kolmogorov-Smirnov test in package
	ctest to avoid rounding errors (PR#1004, follow-up).

    o	Use exact Hodges-Lehmann estimators for the Wilcoxon tests in
	package ctest (PR#1150).

    o	Arithmetic which coerced types could lose the class
	information, for example `table - real' had a class attribute
	but was not treated as a classed object.

    o	Internal ftp client could crash R under error conditions such
	as failing to parse the URL.

    o	Internal clipping code for circles could attempt to allocate
	a vector of length -1 (related to PR#1174)

    o	The hash function used internally in match(), unique() and
	duplicated() was very inefficient for integers stored as
	numeric, on little-endian chips.  It was failing to hash the
	imaginary part of complex numbers.

    o	fifo() no longer tries to truncate on opening in modes
	including "w". (Caused the fifo example to fail on HP-UX.)

    o	Output over 1024 characters was discarded from the GNOME
	console.

    o	rug() now correctly warns about clipped values also for logarithmic
	axes and has a `quiet' argument for suppressing these (PR#1188).

    o	model.matrix.default was not handling correctly contrasts.arg
	which did not supply a full set of contrasts (PR#1187).

    o	The `width' argument of density() was only compatible with S
	for a Gaussian kernel: now it is compatible in all cases.

    o	The rbinom() C code had a transcription error from the original
	Fortran which led to a small deviation from the intended
	distribution. (PR#1190)

    o	pt(t, , ncp=0) was wrong if t was +/-Inf.

    o	Subsetting grouping factors gave incorrect degrees of freedom
	for some tests in package ctests. (PR#1124)

    o	writeBin() had a memory leak.

    o	qbeta(0.25, 0.143891, 0.05) was (incorrectly) 3e-308. (PR#1201)

    o	Fixed alignment problem in ppr.f on Irix. (PR#1002, 1026)

    o	glm() failed on null binomial models. (PR#1216)

    o	La.svd() with nu = 0 or nv = 0 could fail as the matrix passed
	to DGESVD was not of dimension at least one (it was a vector).

    o	Rownames in xcoef and ycoef of cancor() were wrong if x or y
	was rank-deficient.

    o	lqs() could give warnings if there was an exact fit. (PR#1184)

    o	aov() didn't find free-floating variables for Error() terms when
	called from inside another function

    o	write.table() failed if asked to quote a numerical matrix with
	no row names. (PR#1219)

    o	rlnorm( *, *, sd=0) now returns the mean,
	rnbinom(*, *, prob=1) gives 0, (PR#1218).


	**************************************************
	*						 *
	*	       1.3 SERIES NEWS			 *
	*						 *
	**************************************************


		CHANGES IN R VERSION 1.3.1


NEW FEATURES

    o	massage-examples is now a Perl script and about 50x faster.

    o	On Unix(-alike) systems the default pager is now determined
	during configuration, and is `less' if available, otherwise
	`more' (and not `more -s' as previously).

    o	configure now tests for strptime functions that fail on inputs
	before 1970 (found on Irix).  It no longer checks for the SCSL
	and SGIMATH libraries on Irix.

    o	New formula interface to cor.test() in package ctest.

    o	"NA" is now a valid color name (as NA has been a valid integer
	color).

    o	pairs() function has a new `gap' argument for adjusting the
	spacing between panels.

    o	R CMD check has a new test for unbalanced braces in Rd files.

    o	readBin() has a new argument `signed' to simplify reading
	unsigned 8- and 16-bit integers.

    o	New capabilities() option "cledit".

    o	Modified restore code to give clearer error messages in some cases.



BUG FIXES

    o	Fixed placement of mtext() output (including tick labels)
	when text is perpendicular to axis AND axis is logged
	(PR#997 and PR#865).

    o	rect() and arrows() now respond to setting of par(xpd)

    o	abline() now responds to the setting of par(xpd), including
	via the "..." argument (PR#750).

    o	Using cat() to a gzfile() connection no longer compresses poorly
	(at the expense of some latency).

    o	The `exact' p-values for the two-sided two-sample
	Kolmogorov-Smirnov test in 1.3.0 were for the wrong tail.

    o	In the HTML conversion of .Rd files, \link[foo]{bar} was
	ignoring [foo] outside \code{} statements.

    o	lm.influence(), plot.lm(), influence.measures() and the
	related diagnostic measures now handle lm() fits with
	na.action=na.exclude.

    o	Eliminated segmentation fault in while loops without braces
	in their bodies.

    o	barplot did not accept NA heights unless ylim was specified.

    o	predict.lm() failed with single-column model matrix (PR#1018).

    o	legend() now also works with 100s of entries (thanks to
	M. Schlather).

    o	A long-standing bug leading to inaccuracy in polyroot() has been
	fixed (PR#751)

    o	A very old bug with eval() not handling a numeric `envir' argument
	according to specifications has been fixed. [This in particular
	broke ported S-PLUS code that used eval(..., sys.parent())]. Also,
	eval() now checks that a numeric `envir' has length one to prevent
	accidental passing of matrices instead of data frames.

    o	The C code underlying nlm(f, *) now also works correctly when f(x)
	returns +Inf {nlm() itself *did* work!}.

    o	pdfcolor.tex is now included in doc/manual, as pdftex seems no
	longer to include it.

    o	Fixed protect bug in save() code that might have been responsible
	for occasionally saving corrupted workspaces.

    o	capabilities("X11") now reports if X11 is available in this
	session, thereby giving the correct answer if --gui=none was
	specified.

    o	Rd files with ,, inside \code{} were treating this as a
	ligature in LaTeX: now corrected in Rdconv.

    o	dlopen on Compaq Tru64 was finding the wrong entry points:
	worked-around by using different names in the modules.

    o	plot.mts() allows a type argument again (broken in 1.3.0: PR#1010).

    o	scan() has a limit of 8190 on the length of char strings, and
	now warns if it is exceeded (when the string has always been
	truncated).

    o	par adj now accepts values of integer mode (such as text(adj=0:1)).

    o	horizontal adj values outside the range [0, 1] are now
	supported on devices with canHAdj==1 (Windows devices, xfig).

    o	xtabs() without a response was ignoring drop.unused.levels=TRUE.

    o	readLines(ok=FALSE) was not generating an error when it should.

    o	princomp(covmat=) has been broken.

    o	Many documentation clean-ups: formerly undocumented arguments,
	use of T/F rather than TRUE/FALSE.

    o	df[] <- foo now works for data frames (PR#1047).

    o	nargs() was documented incorrectly.

    o	Using seq.POSIXt(by="2 weeks") was stepping by single weeks
	(PR#1046).

    o	dummy.coef.lm was not handling complex terms like z:I(x).
	It now either does or warns and gives NAs (PR#1048).

    o	predict.mlm() was broken (PR#1049).

    o	ksmooth (in package modreg) was using points to the left
	of the kernel under some circumstances (PR#1050).

    o	attr(x, "class") <- character(0) was segfaulting.  Similar problem
	with "comment" attribute also fixed.

    o	loadings() results from PCA (as well as from factor analysis)
	are now printed by print.loadings.

    o	Using chol() on an non-positive-definite matrix gave an
	misleading error message (PR#1061).

    o	as.character() on a language object was truncating to about 70
	characters: the internal limit (from the deparse code) is now the
	maximum possible 500.

    o	X11() device was failing to re-initialize correctly after all
	devices were shut down, so the colortype could not be changed
	and some systems showed protocol errors. (PR#1065)

    o	Converting Inf and NaN values by as.character() and reading by
	scan() was supported by strtod on some platforms and not
	others: these are now handled by R itself. (PR#1072)

    o	hclust(dist(1)) doesn't loop infinitely but signal an error.

    o	cutree() can now cut outside heights and does not return
	garbage	for h >= max(tree$heights) anymore. (PR#1067)

    o	interaction(...,drop=F) returned an object looking like a
	factor, but with storage mode "double", confusing
	model.matrix.default (PR#1003)

    o	splineDesign(*, ord=) and others give better error messages for
	wrong `ord' (and have slightly improved documentation).


		CHANGES IN R VERSION 1.3.0


NEW FEATURES

    o	Changes to connections:

	-  New function url() to read from URLs.  file() will also
	   accept URL specifications, as will all the functions which
	   use it.

	-  file connections can now be opened for both reading and writing.

	-  Anonymous file connections (via file()) are now supported.

	-  New function gzfile() to read from / write to compressed files.

	-  New function fifo() for connections to / from fifos (on Unix).

	-  Text input from file, pipe, fifo, gzfile and url connections
	   can be read with a user-specified encoding.

	-  New functions readChar() and writeChar() to read character
	   strings with known lengths and no terminators, and to write
	   user-specified lengths from strings.

	-  sink() now has a stack of output connections, following S4.

	-  sink() can also be applied to the message stream, to capture
	   error messages to a connection.  Use carefully!

	-  seek() has a new `origin' argument.

	-  New function truncate() to truncate a connection open for
	   writing at the current position.

	-  Socket connections via function socketConnection().

	-  The `blocking' argument for file, fifo  and socket connections
	   is now operational.

    o	Changes to date/time classes and functions:

	-  Date/time objects now all inherit from class "POSIXt".

	-  New function difftime() and corresponding class for date/time
	   differences, and a round() method.

	-  Subtraction and logical comparison of objects from different
	   date/time classes is now supported.	NB: the format for the
	   difference of two objects of the same date/time class has
	   changed, but only for objects generated by this version, not
	   those generated by earlier ones.

	-  Methods for cut(), seq(), round() and trunc() for date/time
	   classes.

	-  Convenience generic functions weekdays(), months(), quarters()
	   and julian() with methods for "POSIXt" objects.

    o	Coercion from real to integer now gives NA for out-of-range
	values, rather than the most extreme integer of the same sign.

    o	The Ansari-Bradley, Bartlett, Fligner-Killeen, Friedman,
	Kruskal-Wallis, Mood, Quade, t, and Wilcoxon tests as well as
	var.test() in package ctest now have formula interfaces.

    o	Matrix multiplication functions %*% and crossprod() now use a
	level-3 BLAS routine dgemm.  When R is linked with the ATLAS
	or other enhanced BLAS libraries this can be substantially
	faster than the previous code.

    o	New functions La.eigen() and La.svd() for eigenvector and
	singular value decompositions, based on LAPACK.	 These are
	preferred to eigen() and svd() for new projects and can make
	use of enhanced BLAS routines such as ATLAS.  They are
	used in cancor(), cmdscale(), factanal() and princomp()
	and this may lead to sign reversals in some of the output of
	those functions.

    o	Provided the Fortran compiler can handle COMPLEX*16, the
	following routines now handle complex arguments, based on
	LAPACK code.

	qr, qr.coef, qr.solve, qr.qy, qr.qty, solve.default, svd, La.svd.



    o	aperm() uses strides in the internal C code and so is
	substantially faster (by Jonathan Rougier).

    o	The four bessel[IJKY](x,nu) functions are now defined for nu < 0.

    o	[dpqr]nbinom also accept an alternative parametrization via the
	mean and the dispersion parameter (thanks to Ben Bolker).

    o	Generalised "birthday paradox" functions [pq]birthday.

    o	boxplot() and bxp() have a new argument `at'

    o	New function capabilities() to report optional capabilities
	such as jpeg, png, tcltk, gzfile and url support.

    o	New function checkFF() for checking foreign function calls.

    o	New function col2rgb() for color conversion of names, hex, or
	integer.

    o	coplot() has a new argument `bar.bg' (color of conditioning bars),
	gives nicer plots when the conditioners are factors, and allows
	factors for x and y (treated almost as if unclass()ed) using new
	argument `axlabels'.  [original ideas by Thomas Baummann]

    o	`hessian' argument added to deriv() and its methods.  A new function
	deriv3() provides identical capabilities to deriv() except that
	`hessian' is TRUE by default.
	deriv(*, *, func = TRUE) for convenience.

    o	New dev.interactive() function, useful for setting defaults for
	par(ask=*) in multifigure plots.

    o	dist() in package mva can now handle missing values, and
	zeroes in the Canberra distance.

    o	The default method for download.file() (and functions which use
	it such as update.packages()) is now "internal", and uses code
	compiled into R.

    o	eigen() tests for symmetry with a numerical tolerance.

    o	New function formatDL() for formatting description lists.

    o	New argument `nsmall' to format.default(), for S-PLUS
	compatibility (and used in various packages).

    o	?/help() now advertises help.search() if it fails to find a topic.

    o	image() is now a generic function.

    o	New function integrate() with S-compatible call.

    o	New function is.unsorted() the C version of which also speeds up
	.Internal(sort()) for sorted input.

    o	is.loaded() accepts an argument PACKAGE to search within
	a specific DLL/shared library.

    o	Exact p-values are available for the two-sided two-sample
	Kolmogorov-Smirnov test.

    o	lm() now passes `...' to the low level functions for regression
	fitting.

    o	Generic functions logLik() and AIC() moved from packages nls
	and nlme to base, as well as their *.lm methods.

    o	New components in .Machine give the sizes of long, long long and
	long double C types (or 0 if they do not exist).

    o	merge.data.frame() has new arguments, `all[.xy]' and `suffixes',
	for S compatibility.

    o	model.frame() now calls na.action with the terms attribute set
	on the data frame (needed to distiguish the response, for
	example).

    o	New generic functions naresid(), napredict() and naprint()
	(formerly in packages survival5 and MASS, also used in rpart).
	Also na.exclude(), a variant on na.omit() that is handled
	differently by naresid() and napredict().

	The default, lm and glm methods for fitted, residuals, predict
	and weights make use of these.

    o	New function oneway.test() in package ctest for testing for
	equal means in a one-way layout, assuming normality but not
	necessarily equal variances.

    o	options(error) accepts a function, as an alternative to
	an expression.	(The Blue Book only allows a function; current
	S-PLUS a function or an expression.)

    o	outer() has a speed-up in the default case of a matrix outer
	product (by Jonathan Rougier).

    o	package.skeleton() helps with creating new packages.

    o	New pdf() graphics driver.

    o	persp() is now a generic function.

    o	plot.acf() makes better use of white space for `nser > 2', has
	new optional arguments and uses a much better layout when more
	than one page of plots is produced.

    o	plot.mts() has a new argument `panel' providing the same
	functionality as in coplot().

    o	postscript() allows user-specified encoding, with encoding files
	supplied for Windows, Mac, Unicode and various others, and with
	an appropriate platform-specific default.

    o	print.htest() can now handle test names that are longer than
	one line.

    o	prompt() improved for data sets, particularly non-dataframes.

    o	qqnorm() is now a generic function.

    o	read.fwf() has a new argument `n' for specifying the number of
	records (lines) read in.

    o	read.table() now uses a single pass through the dataset.

    o	rep() now handles lists (as generic vectors).

    o	scan() has a new argument `multi.line' for S compatibility,
	but the default remains the opposite of S (records can cross
	line boundaries by default).

    o	sort(x) now produces an error when x is not atomic instead of
	just returning x.

    o	split() now allows splitting on a list of factors in which case
	their interaction defines the grouping.

    o	stl() has more optional arguments for fine tuning, a summary()
	and an improved plot() method.

    o	New function strwrap() for formatting character strings into
	paragraphs.

    o	New replacement functions substr<-() and substring<-().

    o	Dataset swiss now has row names.

    o	Arguments `pkg' and `lib' of system.file() have been renamed to
	`package' and `lib.loc', respectively, to be consistent with
	related functions.  The old names are deprecated.  Argument
	`package' must now specify a single package.

    o	The Wilcoxon and Ansari-Bradley tests now return point
	estimators of the location or scale parameter of interest along
	with confidence intervals for these.

    o	New function write.dcf() for writing data in Debian Control File
	format.	 parse.dcf() has been replaced by (much faster)	internal
	read.dcf().

    o	Contingency tables created by xtabs() or table() now have a
	summary() method.

    o	Functions httpclient(), read.table.url(), scan.url() and
	source.url() are now deprecated, and hence method="socket' in
	download.file() is.  Use url connections instead: in
	particular URLs can be specified for read.table(), scan() and
	source().

    o	Formerly deprecated function getenv() is now defunct.

    o	Support for package-specific demo scripts (R code).  demo() now
	has new arguments to specify the location of demos and to allow
	for running base demos as part of `make check'.

    o	If not explicitly given a library tree to install to or remove
	from, respectively, R CMD INSTALL and R CMD REMOVE now operate
	on the first directory given in `R_LIBS' if this is set and
	non-null, and the default library otherwise.

    o	R CMD INSTALL and package.description() fix some common problems
	of DESCRIPTION files (blank lines, ...)

    o	The INSTALL command for package installation allows a `--save'
	option.	 Using it causes a binary image of the package contents
	to be created at install time and loaded when the package is
	attached.  This saves time, but also uses a more standard way
	of source-ing the package.  Packages that do more than just
	assign object definitions may need to install with `--save'.
	Putting a file `install.R' in the package directory makes
	`--save' the default behavior.	If that file is not empty, its
	contents should be R commands executed at the end of loading
	the image.

	There is also a new command line option `--configure-vals' for
	passing variables to the configure script of a package.

    o	R CMD check now also checks the keyword entries against the list
	of standard keywords, for code/documentation mismatches (this
	can be turned off by the command line option `--no-codoc'), and
	for sufficient file permissions (Unix only).  There is a new check
	for the correct usage of library.dynam.

	It also has a new command line option `--use-gct' to use
	`gctorture(TRUE)' when running R code.

    o	R CMD Rd2dvi has better support for producing reference manuals
	for packages and package bundles.

    o	configure now tests for the versions of jpeg (>= 6b), libpng (>=
	1.0.5) and zlib (>= 1.1.3).  It no longer checks for the
	CXML/DXML BLAS libraries on Alphas.

    o	Perl scripts now use Cwd::cwd() in place of Cwd::getcwd(), as
	cwd() can be much faster.

    o	R::Dcf.pm can now also handle files with more than one record
	and checks (a little bit) for continuation lines without leading
	whitespace.

    o	New manual `R Installation and Administration' with fuller
	details on the installation process: file `INSTALL' is now a
	brief introduction referencing that manual.

    o	New keyword `internal' which can be used to hide objects that
	are not part of the API from indices like the alphabetical lists
	in the HTML help system.

    o	Under Unix, shlib modules for add-on packages are now linked
	against R as a shared library (`libR') if this exists.	(This
	allows for improved embedding of R into other applications.)

    o	New mechanism for explicitly registering native routines in a
	DLL/shared library accessible via .C(), .Call(), .Fortran() and
	.External().  This is potentially more robust than the existing
	dynamic lookup, since it checks the number of arguments, type of
	the routine.

    o	New mechanism allowing registration of C routines for converting
	R objects to C pointers in .C() calls.	Useful for references to
	data in other languages and libraries (e.g. C and hdf5).

    o	The internal ftp/http access code maintains the event loop, so
	you can download whilst running tcltk or Rggobi, say.  It can
	be hooked into package XML too.



BUG FIXES

    o	boxplot.stats() now returns the correct `n' component in the case of
	NAs. This also affects `conf', the notch length (PR#967).

    o	the "coef = 0" fix (PR#917) to boxplot.stats() broke
	boxplot.stats(do.out = FALSE).

    o	curve(* , add = FALSE) now works correctly again if used when
	par("xlog") is true.

    o	Printing a dataframe with a column called "row.names" or
	"check.names" omitted the column.

    o	data.frame(a=1, b=2)[1, -(1:2)]	 now works, giving an empty
	data frame.  as.matrix(df), deparse(), dput() and str() now work
	for empty data frames.

    o	dbeta() could return zero erroneously on some platforms where
	roundoff makes e.g. 1.3 - 1 > (1.3 + 1) - 2 (Solaris and HP-UX
	were affected). (PR#970)

    o	pointer protection in deriv() (PR#953)

    o	expand.data.frame() didn't interpret its subset= argument in
	the data frame. (PR#979 et al., fix from Greg Warnes)

    o	format() on character arrays was losing the dimensions.

    o	hist.default() was ignoring its `probability' argument for
	equi-spaced breaks.

    o	Occasionally insane results of is.nan(NULL), is.na(NULL) (PR#952)

    o	ks.test() in package ctest now had the one-sided alternatives in
	the one-sample case reversed (PR#934).

    o	ls.str() and lsf.str() now work better with pos > 1, and are
	correctly documented (PR#899).

    o	plot(1:2, xaxs = "i") now gives both "1.0" and "2.0" x-axis labels.

    o	promax() was not using its `m' argument (m=4 was always used).

    o	qr.X() was ignoring pivoting (which happens only in
	rank-deficient cases).

    o	sign of Pearson residuals was wrong for reciprocal link (PR#862)

    o	The algorithm for determining starting estimates in the SSfpl
	self-starting model in the nls package was changed following a
	suggestion by Phillipe Grosjean <phgrosje@ulb.ac.be>

    o	svd(x)$v was not a matrix when x had only 1 row (PR#963).

    o	symnum(x) behaves more reasonably for zero length or non-numeric x.

    o	The implementation of sys.function() did not work when the
	current function was already a function (e.g., a closure).

    o	tapply() had "..." argument after simplify=, which made it
	incompatible with S when passing additional unnamed arguments to FUN.

    o	use formula environments in xy.coords() (PR#932)


    o	Unused entry points in `src/appl/fortran.c' and `Fortran.h'
	have been removed.

    o	Unused directory `src/f2clib' and header `src/include/R_ext/f2c.h'
	have been removed.

    o	The documentation and parts of the parse/deparse mechanism
	indicated that there was an operator `%'. Corrected (PR#925).

    o	Fixed some cases where the deparser gave code that threw a
	syntax error when parsed.

    o	Using a pushback with more than two lines at a time could crash.

    o	Eliminate or warn on use of .Last.value in help examples, since
	.Last.value is only set from top-level expressions (and was
	incorrectly documented).

    o	asInteger was ignoring integer overflow (PR#929 and others).

    o	approxfun(*, ties = <fun>) could return garbage when there were ties;
	ties = "ordered" was incorrect--also for approx()-- when there was
	a tie at the very right.


	**************************************************
	*						 *
	*	       1.2 SERIES NEWS			 *
	*						 *
	**************************************************


		CHANGES IN R VERSION 1.2.3

NEW FEATURES

    o	Support for configuration and building the Unix version of R
	under Mac OS X.	 (The `classic' Macintosh port is `Carbonized'
	and also runs under that OS.)

    o	dotchart() and stripchart() become the preferred names for
	dotplot() and stripplot(), respectively.  The old names are now
	deprecated.

    o	Functions in package ctest now consistently use +/-Inf rather
	than NA for one-sided confidence intervals.



BUG FIXES

    o	`Writing R Extensions' incorrectly described an entry point
	`fmod' which was not included in the R binary on most systems.
	The entry point has been removed, to avoid any confusion with
	the standard C entry point of the same name.

    o	Printing of kernels in package ts was unreliable: the internal
	representation was correct.

    o	A problem with "..." in substitutions has been fixed (PR#860).

    o	Various strangeness with match.call() and "..." has been fixed
	(PR#813).

    o	sys.function() could return an unevaluated promise, messing up
	formals() and match.arg() (PR#872)

    o	Deparsing or dumping attributes with non-standard names was
	not quoting the name (PR#871).

    o	We now use match.fun() in tapply() so that it won't get trapped
	by non-functions masking FUN.

    o	The `nmax' argument in scan(what=list(...), nmax=300) was
	counting blank lines, although they were said to be ignored.
	This affected using read.table on files with blank lines in
	1.2.2, and using `n' with `what' a list.

    o	as.numeric(), as.integer(), as.complex() returned zero on
	completely blank strings. Now they return NA. (PR#870)

    o	Overflow in deparse() in terms(formula) with very long left-hand
	side fixed.  (PR#873)

    o	lowess(c(1:3, 7:5)) now should give the same on different platforms,
	since now in the C code (int)(f*n + 1e-7) is used.

    o	curve(*, add = TRUE) now works properly with active log scales.

    o	rt() could give different results on different platforms as
	the order of evaluation of calls to random numbers was not
	fully defined.	This affected the Mac port.

    o	ppr() inside nested calls sometimes failed to find objects
	due to a typo in the eval call in ppr.formula.

    o	qchisq(0.025, 31, ncp=1, lower.tail=FALSE) now works.  (PR#875)

    o	dchisq with integer x, df and ncp sometimes gave incorrect
	results on i686 Linux.

    o	Cancelling a quit caused quit() not to ask next time it was called.

    o	Some complicated operations with "..." didn't work.

    o	Missingness was not correctly propagated in some cases.

    o	eigen() segfaulted on 0-dimensional matrices.

    o	nls( ~ rhs, ..)	 now works (formula with empty left hand side).

    o	The fuzz added in hist() for 1.2.2 broke the logic testing for
	equidistant breakpoints.

    o	Calls to replacement functions ("f<-") lost argument names
	(PR#888).

    o	is.na() and is.nan() gave random results on lists containing
	zero-length objects.

    o	cor(), cov() and var() gave a result on a zero-length argument
	(now an error).	 cov(x, NULL) and cor(x, NULL) are now errors
	if x is a vector.  (PR#883).

    o	?smooth.spline now properly describes `spar' which is *not*
	lambda.	 smooth.spline(1:20, spar = 50) gives an error instead
	of silent nonsense.  print.smooth.spline() now makes use of a
	digits argument.

    o	Confidence intervals for wilcox.test() had the samples reversed
	in the two-sided case (PR#895), and sometimes got continuity
	correction wrong (PR#896).

    o	Using out-of-range font values in text() on a postscript()
	device on Windows could crash.	.ps.prolog was incorrectly
	named in some of the documentation.  (PR#914)

    o	Warning messages of > 8191 chars could crash R (PR#902), as
	could errors.  Now they are truncated to 8191 chars on
	machines which have vsnprintf (almost all).

    o	range() now works properly for date-time objects.

    o	contour() could loop infinitely (PR#897).

    o	R-lang manual had precedence of %% wrong (PR#879).

    o	try() constructs lost protection of R_alloc'ed memory (PR#877).

    o	Documented that as.numeric() dispatches to as.double.foo methods
	(PR#918.1).

    o	httpclient() (and the "socket" method of download.file) skipped ^V
	rather than ^Z in input (if drop.ctrl.z = TRUE, the default).

    o	boxplot(*, range = 0) and boxplot.stats(*, coef = 0) now
	don't return outliers anymore (PR#917).

    o	segmentation fault with tmp[[1,]] (PR#904)

    o	incorrect "..." handling in plot.factor (PR#830)



		CHANGES IN R VERSION 1.2.2


NEW FEATURES

    o	The Macintosh port becomes a full member of the R family and its
	sources are incorporated as from this release.
	See `src/macintosh/INSTALL' for how that port is built.

    o	The API header files and export files `R.exp' are released under
	LGPL rather than GPL to allow dynamically loaded code to be
	distributed under licences other than GPL.

    o	postscript() and xfig() devices now make use of genuine Adobe
	afm files, and warn if characters are used in string width or
	height calculations that are not in the afm files.

    o	Configure now uses a much expanded search list for finding a
	FORTRAN 77 compiler, and no longer disallows wrapper scripts for
	this compiler.

    o	New Rd markup \method{GENERIC}{CLASS} for indicating the usage
	of methods.

    o	print.ftable() and write.ftable() now have a `digits' argument.

    o	undoc() has a new `lib.loc' argument, and its first argument is
	now called `package'.


BUG FIXES

    o	The behaviour of polygon() with NA coordinate values is now
	documented.

    o	polygon() now correctly recycles the values of border and lty.
	Thanks to Denis White.

    o	readBin() and writeBin() were not always making good use of
	long types (such as long double) when available.

    o	The C function fprec was not handling very small denormalized
	numbers correctly.  This affected the way they were printed on
	Windows, for example.

    o	legend() now draws points after lines allowing "empty dots on
	lines" thanks to Ben Bolker.

    o	Setting row/column names preserves the names of the dimnames
	(PR#809).

    o	Using help() after help.start() on Unix was failing to find
	the linked help files if more than one package was loaded (as
	now happens by default).

    o	scan now sets the maximal sizes internally when `what' is a list
	from `nmax' and failing that `nlines'.	This uses memory much
	more efficiently if `nmax' is specified.  read.table() makes use
	of this.

    o	The FORTRAN code used is now much closer to ANSI compliance.

    o	cov.rob() gives a useful error message on nearly-degenerate
	matrices.

    o	summary() on a data frame was computing results to a precision
	based on options("digits") (default 4), not its `digits'
	argument.  Now results are computed to full precision but
	formatted using `digits'.

    o	summary(m, digits=*) also properly works for matrices.

    o	When returning parameters from .C/.Fortran, the OBJECT field was
	not copied even though class attributes were (PR#834).

    o	There was a spurious warning from the X11 driver on 100 dpi
	displays (PR#840, fix from Tom Vogels).

    o	scan() was reading all-blank numeric fields as zero.
	Should be read as NA, and are now.

    o	dnbinom(*, size, *) now works again for size < 1 (PR#842).

    o	dgeom(*, p = 0) and pgeom(*, p = 0) don't give NaN anymore.

    o	smooth.spline() allows zero weights again.

    o	aperm() fix for list arg; aperm(*, resize=FALSE) now works with
	dimnames (by dropping them).

    o	The xfig() driver was not closing unclosed polygons as the R
	driver expected (but did not document).

    o	spec.ar() now handles order 1 correctly.

    o	Add fuzz to prevent anomalies with hist().

    o	print.matrix() checks length of rowlab, collab (PR#850)

    o	add1.glm() was using the wrong weights for binomial glms in
	cbind(successes, failures) ~ lhs  form, since 1.2.0.

    o	Eliminate packing of the `structRstart' structure, which was
	probably non-ISO C and caused some compilers problems (PR#852).

    o	all.vars() no longer returns empty `names' (PR#829).

    o	dotplot() passes `cex' down to the mtext() calls used for the
	labels (PR#816).

    o	The pictex() driver was drawing polylines incorrectly (PR#845).

    o	In the event of a fatal X11 error (this can be generated under FVWM
	by selecting Destroy), the input handler would loop, leaving the
	"please save work and shut down R" advice useless. There should now
	be an opportunity for a relatively graceful exit.

    o	polyroot() misbehaved if all coefficients except that of the highest
	degree term were zero (partial fix for PR#751)

    o	spline(method="natural") was extrapolating incorrectly (both
	to the left and to the right, for different reasons).  (PR#653)

    o	Line clipping was incorrect for log-plots. (PR#839)

    o	Add explicit test for rank-deficient residuals to summary.manova().

    o	The help search databases did not contain the data from the
	platform-specific help files.

    o	parse.dcf() and hence package.contents() now work with a warning
	for empty contents' files.

    o	which.min() and which.max() now properly work for 0-length and
	NA-only arguments.



		CHANGES IN R VERSION 1.2.1


NEW FEATURES

    o	New functions factanal(), varimax(), promax() and examples in
	package mva.

    o	New functions readBin() and writeBin() to transfer binary data
	to and from connections.

    o	merge() is partially moved to C to reduce its memory usage.

    o	library(help = PKG) now displays the contents of the package's
	DESCRIPTION file in addition to its INDEX.

    o	Sd2Rd can handle S4-style documentation too: see `Writing R
	Extensions'.

    o	prompt() now also works with a character argument (useful for
	producing many *.Rd files in a loop).

    o	The Unix front-end shell script now ignores a value for R_HOME
	found in the environment.

    o	Connections functions such as file() now accept a description of
	length > 1, with a warning.

    o	All text-mode connections now accept input with LF, CR or CRLF
	line endings.  This means that readLines() can be used on DOS
	files and source() on Mac files, for example.

	Also, CRLF-terminated files can be used as stdin on Unix, and
	files with last lines without an EOL mark can be used as stdin
	and source()-ed on Unix and Windows.

    o	DESCRIPTION file has a new recommended `Maintainer:' field.

    o	stars() now uses a larger "cex" for the labels, and cex and lwd
	are now arguments. Further, the argument names (xlim, ylim,
	axes) are now consistent with other plot functions.  The key symbol
	is not clipped anymore into the plot region by default.

    o	Date-time quantities are now printed with the timezone, if known.

    o	R CMD build now ignores all files specified (via Perl regexps)
	in file `.Rbuildignore' in the top-level source	directory of a
	package.

    o	Horizontal boxplots are possible with  horizontal = TRUE.

    o	all.equal() on lists now compares them as generic vectors, that
	is they are equal if have identical names attributes and
	all components are equal.

    o	Invalid lines in .Renviron now give warnings when R is started.

    o	Argument `na.last' implemented for rank().


BUG FIXES

    o	There have been many small improvements/corrections in the
	documentation. In particular:

	The help pages for lm and glm now describe the fitted objects.

	is.vector() is now correctly documented: complex vectors and
	lists return TRUE.

    o	The default sortedXyData constructor in the nls package now
	handles missing values in the response.

    o	On startup, file .RData is now restored *after* the site and
	user profiles are loaded (if at all).  This is as previously
	documented.

    o	as.POSIXlt (and *ct) operating on a character string
	only extracted the date (and not the time) in some cases.

    o	as.POSIXct() on character objects was ignoring `tz'.

    o	codoc(ignore.generic.functions = TRUE) works again.

    o	Explicitly close files opened by sink() for OSes (such as
	Windows) that benefit from it.

    o	Prevent closing the sink connection (which would be a silly
	thing to do).

    o	showConnections(all = TRUE) was sometimes counting connections
	incorrectly, and so not showing some closed ones.

    o	ts(1:10, start= c(1999,6), end = c(2000,3), frequency = 12)
	now prints both years (as it should).

    o	Monthly multivariate time series now print proper month names
	in all cases.

    o	print.stl(), print.princomp() and print.prcomp() now pass on
	`digits =' etc.

    o	prompt() now produces a \usage{} line for data frames and
	other datasets, as documented in `Writing R Extensions'.

    o	glm() now returns correct linear predictor and fitted values
	for zero-weight cases.

    o	scan(strip.white=TRUE) and readline() could give incorrect
	answers when an input field was empty or blank.

    o	dchisq() now behaves better for large values of its ncp parameter.

    o	besselJ(*, nu) is now ok for nu < 1; fix improves accuracy of
	other values by a few bits as well.

    o	The convergence criterion in the Fortran SVD code has been
	changed to circumvent spurious convergence errors when
	comparing extended-precision quantities on ix86 Linux (and
	some compilers and options).

    o	Rdindex now handles multi-line \title{}'s correctly.

    o	Add weights.glm() so that plot.lm() gets the correct weights from
	glm objects (the ones that go with deviance residuals not the
	working residuals).

    o	Printing a language object (e.g. a formula) in a list was
	clobbering the buffer holding the tag labels which then were
	lost in subsequent lines of printout (PR#746).

    o	aic in family() objects is now computed more precisely using
	dxxxx(log=TRUE).  For binomial fits the value was wrong for
	models specified via proportions and weights (PR#796).

	Avoid NaN values in aic where n = 0 occurs.

    o	Using non-integer numbers of successes in a binomial glm (as
	formerly in demo(lm.glm)) now gives a warning, as the theory and
	in particular the AIC value is not applicable.

    o	demo(is.things) works again {is.ALL() doesn't call methods
	anymore}.

    o	persp(*, nticks = nn) now works (better) for too small nn.
	persp(*, main = t1, sub= t2) now work (as always documented).

    o	Printing of attributes of a list element no longer precedes
	`attr' by the tag (PR#715).

    o	It is no longer possible to use df[foo] to select non-existent
	columns in df and so create an invalid object of class
	"data.frame" (PR#698).

    o	edit.data.frame() was trying to set row.names on a list, which
	is no longer allowed.

    o	In the \link[pkg]{topic}, `pkg' was not being used if `topic'
	was found in a package in .lib.loc.  Now `pkg' is always used.

    o	plot() with small relative ranges gave an error, which e.g. broke
	library(ts); plot(stl(ts(rep(1:7, 15), freq = 7), s.win = "per"))

    o	Using scan() with a 0-length `what' argument now gives an error
	message rather than a segfault.

    o	Loading .Random.seed could extremely rarely and with some
	generators reject a value as NA_INTEGER when it was valid.

    o	save(..., ascii=TRUE) created broken files when saving strings
	containing special characters (ASCII code > 127).

    o	mean(c(1,NA,NA,NA)[-1], trim = .1, na.rm = TRUE) doesn't give an
	error anymore.

    o	As the supplied afm files are not properly in the ISOLatin1
	encoding, the font metric for "-" was wrong since 0.63 on a
	postscript/xfig device, and randomly wrong in 1.2.0.  It will
	now be correct (but the files remain incorrect: C45 is "minus"
	not "hyphen" and there are missing slots).

	Metrics for the duplicated characters (acute, dieresis,
	macron, space) in ISOLatin1 encoding are now correct for both
	occurrences: previously only one was present.

    o	The data-time functions try harder to guess the DST setting
	when the OS does not know, as some OSes were printing times
	in DST if this was marked as unknown.

    o	Setting par(pty=) after par(pin=) or par(plt=) was having no
	effect until the margins were set.

    o	Nested \describe sections in .Rd files have (again) nested
	indentation when converted to text.

    o	Concatenation of C strings by ## is no longer used, to avoid
	spurious warnings from some recent versions of gcc.

    o	dev.copy2eps() allows a `paper' argument to be passed to
	postscript().

    o	file.show() handles the case of zero files better.

    o	formula.lm uses object$formula if it exists, in preference
	to object$terms.

    o	strsplit() is corrected for an empty split pattern.

    o	kronecker() now does a better job when creating dimnames.

    o	Better handling of input dimnames in fourfoldplot().



		CHANGES IN R VERSION 1.2.0


NEW FEATURES

    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
	allowed.

    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
	manual.

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

    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
	environment.

    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
	collection.

    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
	outline.

    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
	manipulations.

    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
	splitting.

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

    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 package 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 be replaced by
	formula(terms.object).

    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
	tabulation.


    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
	structures.

    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
	library.

	There is also a linker front-end `R CMD LINK' which is useful
	for creating executable programs linked against the R shared
	library.


BUG FIXES

    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
	data.

    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()
	(PR#757)

    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
	1e-305.

    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.



	**************************************************
	*						 *
	*	       1.1 SERIES NEWS			 *
	*						 *
	**************************************************


		CHANGES IN R VERSION 1.1.1


NEW FEATURES

    o	data(), example() and help() now search the loaded packages, then
	in their .lib.loc argument, the latter as pre-0.99.0.  See
	their help pages for the precise details.

    o	help() has a new argument `try.all.packages' set by the option
	"help.try.all.packages". If help is not found in the normal
	path and this is TRUE then a search is made of all packages
	for possible matches.

    o	Improved detection of Tcl/Tk at configure time.	 One can either
	set configure variables TCLTK_CPPFLAGS and TCLTK_LIBS, or give
	the locations of the tclConfig.sh and tkConfig.sh scripts via
	the `--with-tcl-config' and `--with-tk-config' arguments.

    o	prop.trend.test() - test for trend in proportions.

    o	write.table() has new argument `dec' for setting the decimal
	separator (SPSS/Windows and probably others want commas in
	continental European locales).

    o	Advance warning: save(, oldstyle=TRUE) will no longer be
	available after this release.

    o	Symbols can now be coerced to expressions, making
	as.expression(quote(a)) work


BUG FIXES

    o	data() now works correctly with data-only packages.

    o	Standalone Mathlib can now be made if builddir = srcdir
	(working around an undocumented autoconf `feature').

    o	Check for pre-1.1.0 saved object .Postscript.options in postscript().

    o	More stringent checks on the arguments to dataentry().

    o	Specifying xlab as an expression now works again.

    o	dev2bitmap() works again.

    o	Numerous uses of `F' and `T' replaced by `FALSE' and `TRUE'.

    o	bxp() now extends `ylim' properly when notch=TRUE (and a
	notch is more extreme than other stats).
	Also, varwidth is okay again, see example(split).

    o	Making manuals without making R first now works.

    o	princomp() now works when some eigenvalues are tiny negative
	values (which are treated as zero).

    o	SearchEngine.html was not installed when builddir != srcdir.

    o	lm.{w}fit(x,y,..) now work when x has no column names.
	These functions no longer add and subtract n zeros when there's no
	offset.	 They are now documented somewhat.

    o	Some HTML files used src="R.css" instead of href="R.css" causing
	some browsers to ignore the style sheet.  `R.css' now passes the
	w3c CSS validator and gives the intended results with Internet
	Explorer.  `R.css' is copied to all library directories.

    o	The data editor no longer crashes when entries contain more than
	45 characters, and works correctly if the field width is
	larger than the window width.

    o	Recording plots used to ignore graphics events before the last
	replay.

    o	plot(), points(), etc now give warnings and error for invalid
	`type' arguments.

    o	matplot() now allows the same `type's as plot().

    o	dev.print() and dev.copy2eps() now work when called from a
	function, such as dev2bitmap().

    o	anova.glmlist works correctly with decreasing models and
	test="F" now gets the correct residual df.

    o	Functions created (not just edited) with fix() now get
	environment .GlobalEnv not the body of fix.

    o	Rdconv was ignoring OS-specific parts of the files with some
	Perl versions. (This did not affect installing packages.)

    o	R CMD check  did not run more than one specific test.

    o	keyword2html omitted items when changing up a level, so
	the HTML search engine keyword list was missing `data' and
	`utilities', for example.

    o	aov() with multiple strata was setting some spurious options.

    o	Under UNIX, help(, htmlhelp=TRUE) uses the linked copy of the
	HTML file in ~/.R if help.start() has been run recently in the
	session, so the style sheet and hyperlinks should now be found.

    o	dotplot's arguments `color' and `lcolor' are now interpreted
	correctly if they are vectors of length > 1.  (It is not clear
	from the help that this was ever intended.)

    o	Error messages of e.g. do.call() are now spaced properly.

    o	summary(.matrix | .data.frame) now respects a `digits' argument.

    o	scan() recognises quoted strings by default again. The default
	for the quote= argument got set wrongly when it was
	introduced. They are, however, turned off when using sep="\n",
	since you probably want unprocessed lines of text in that
	case.

    o	fixed buglet where scan() would double a character following a
	terminating quote symbol.

    o	kmeans was failing on vector inputs (although not documented
	to accept such).

    o	fixes in predict.lm (John Maindonald)

    o	NCOL got confused by 1D arrays, which it now reports have 1
	column rather than NA.

    o	rep(1:2,c(1,-1)) segfaulted (PR 619)

    o	x[["a"]] <- y rejected some object types for y (e.g.
	expressions) which were accepted in x$a <- y (PR

    o	data editor froze on empty data frame, and more generally on
	zero-length cols.

    o	data editor did not handle factors properly in numeric-edit
	mode.

    o	table() misbehaved on empty (or all-NA) data

    o	data editor now handles empty data frames, allowing data entry
	to begin with  dd<-edit(data.frame())  or
	dd<-data.frame() ; fix(dd)

    o	plotting math expressions when specified as a LANGSXP or
	SYMSXP didn't work in several cases: plot(1,main=quote(a))
	would segfault and there were problems with title(), text(),
	and mtext() as well.

    o	optim(): no more segfault for REPORT=0; corrected error msg; ..
	maxit default is now okay also when "L-*-B" is chosen automatically.
	Using (abs|rel)tol with that method now gives a warning.

    o	text() did not respect its `xpd' argument, the default of which
	is still to use par("xpd"); gave a wrong error message in one case.

    o	polygon() had an incorrect documentation and silently disregarded
	"..." arguments.

    o	predict.loess was giving incorrect results (those for the
	non-robust fit) in the case of a fit with family = "symmetric"
	and surface = "direct" and prediction with se = FALSE.	The
	fitted values were missing for such fits.

    o	Better rendering of ^ and ~ in latex in \code{} (and they should
	not appear outside code and verbatim sections).

    o	Fixed unterminated string problem with lty (PR 584)

    o	Fixed scoping problem with quasi() family (PR 614)


		CHANGES IN R VERSION 1.1.0


NEW FEATURES


    o	There are several changes to the compile and link flags, and
	an attempt is made to use /usr/local/include and
	/usr/local/lib on all platforms.  Please read config.site and
	INSTALL if you have set flags for previous versions.

    o	New package tcltk, providing interface and language bindings for
	the Tcl/Tk graphical interface toolkit. This makes it possible
	to do some rather nifty things with buttons and entry fields
	and so forth in very few lines of code.	 It is still somewhat
	experimental so don't go churning out thousands of lines of
	GUI code and then blame us for changing the API later on. It does
	not currently work with GNOME because of event loop differences.
	See demo(tkttest) and demo(tkdensity).

    o	Internally using global R_Expressions [getOption("expressions")]
	dramatically speeds up eval.c.

    o	The X11 support code is now in a separate shared library, and
	option `--gui=none' will run R without X11 support (and so x11()
	and data.entry() will not be available).  R BATCH sets --gui=none.

    o	Configuring without X (e.g., `--without-x') does work (at last).
	configure will report if X11 support has been included.
	If R has been built without X11 the default GUI is "none".

    o	GNOME support files have moved from src/gnome to src/unix/gnome
	and the code is now in a separate shared library.  Both
	`--gui=GNOME' and `--gui=gnome' are allowed.

	The main graphics device for use with GNOME is now called
	gtk(); the x11() device from the X11 support can also be used.
	(The gnome() device remains unreliable, and is by default
	unavailable.)

	All GNOME support now installs in R_HOME/gnome to make it
	easier to package separately.

    o	Command line option `-g' can now be used as short version of
	`--gui'.

    o	The "keep.source" option now defaults to interactive()
	instead of TRUE.

    o	Many interface enhancements to the data editor, which now uses
	(by default) variable-width columns and much less redrawing.
	See ?dataentry for a description of the current user interface.

    o	R under Unix can be sent SIGUSR1 to quit and save or SIGUSR2
	to quit and save without running .Last and on.exit
	expressions.

    o	Added ability to use the graphics device driver to perform
	horizontal justification of strings.  This is used in the
	x11(), windows(), postscript() and xfig() drivers and will
	lead to more accurate placing of centred or right-justified
	strings.

    o	Formulas created with the tilde operator now contain the
	environment in which they were created.	 The environment of a
	formula can be accessed with the environment() function.  This
	facility is still experimental; it is intended to help
	simplify writing modeling functions.


    o	$ and $<- are now generic functions.

    o	add1.glm() and drop1.glm() now allow test="F", which is
	appropriate for models with estimated dispersion.

    o	approx() and approxfun() have an extra argument ties= to control
	handling of tied x values

    o	New function as.symbol(), identical to as.name().
	is.symbol and is.name() are now identical by definition;
	before, they were equivalent by implementation.

    o	attach() now works for R data files.

    o	axis() now has additional arguments.  The argument "tick" turns
	tick drawing on and off (on by default).  Additional arguments
	line, pos, and outer; allow more flexible placement of axes.

    o	New device bitmap(), like dev2bitmap() but a stand-alone device.

    o	boxplot() returns (and bxp() accepts) a list containing the summary
	statistics for the boxes (changed from a list of elements one for
	each box).

    o	file="|cmd" is allowed (to pipe output to `cmd'), under cat()
	and postscript() and functions that use them (for example, write()).

    o	New functions chartr() for general-purpose character translation
	in character vectors, and tolower() and toupper() for converting
	alphabetic characters to lower-case and upper-case, respectively.

    o	coplot() has new option subscripts=TRUE to pass the indices
	to the panel function.

    o	cor.test(method="spearman") might give slightly better P values,
	since it now relies on pnorm() (with proper tail) instead of alnorm.

    o	dbinom() works for size=0 (where appropriate).

    o	New trivial function det() for determinant computation
	(the example in ?qr did not seem to be sufficient).

    o	If present in the package, a function .Last.lib will be called
	when a package is detached.

    o	New function dev.copy2eps() copies the current device to an eps
	file, taking the size from that of the device.

    o	dev.print() now prints if possible, and takes the size from
	the device being copied.

    o	edit() or fix() applied to a numeric or character matrix now
	uses the data editor, if available.

    o	edit.data.frame() edits factors in character mode by default,
	and will allow the row names to be edited, by default if they
	are not 1:nrow(name).

    o	expand.model.frame() for adding variables to a model frame.

    o	The handling of estimating the dispersion in glm() fits has been
	changed for consistency across methods.	 For `binomial' and
	`poisson' families the dispersion is always taken as one.
	For `quasibinomial' and `quasipoisson' families it is always
	estimated (by residual chisq/residual df).

    o	Using "~" when specifying lib.loc (for example to help() or
	library()) is now supported.

    o	image() has a new argument "breaks" and divides the zlim range
	into equal-length intervals.

    o	install.packages() and update.packages() have a new `destdir'
	argument for the directory to which to download the packages.

    o	New function interaction.plot().

    o	Internal cleanup of lapply()'s C code.

    o	library(), require(), and sys.source() have a new argument
	` keep.source = getOption("keep.source.pkgs") '.
	This defaults to false, but can be set (also for base) to true
	by setting the environment variable R_KEEP_PKG_SOURCE to "yes"

    o	Par `lty' in lines() now defaults to par("lty") not "solid",
	for consistency with plot().

    o	list.files() [aka dir()]: path argument has now default = "."

    o	locator() allows inline graphics parameters (for the plotting
	it does with type !="n").

    o	New function max.col() from MASS, thanks to V&R.

    o	nlm() can now take additional arguments in ... to be passed to f.

    o	par() returns elements in alphabetical order, and "ann" as a
	logical (not integer).

    o	.Platform has a new component GUI specifying the GUI in use
	(which might be "unknown").

    o	plot.formula() searches for a plot method for the left-side of the
	formula before searching for a plot method for the right-side of
	the formula.

    o	New bitmap devices png() and jpeg() on Unix/X11. (They were
	already available on Windows.)

    o	postscript(print.it=TRUE) now does print the plot file.
	postscript(onefile=FALSE) now produces multiple separate files.

    o	provide() is now deprecated.

    o	New function quade.test() in package ctest for the Quade test
	for unreplicated blocked data.

    o	quantile(x, probs) now propagates NA/NaN in probs.

    o	Option for user-supplied normal random generator in RNGkind().

    o	read.fwf() is no longer dependent on Perl.

    o	New arguments check.names and strip.white to read.table() and
	friends.

    o	Functions recordPlot() and replayPlot() save a plot to an R
	variable and replay it.

    o	residuals.lm() also allows types "partial" and "response"
	as residuals.glm().

    o	Added col option to rug().

    o	scale() is now generic with scale.default method.

    o	New "call. = TRUE" argument for stop(), and
	new function  stopifnot(.) -- to be used in "make check".

    o	str(.) has a new optional argument "nchar.max = 128" and truncates
	strings longer than that.  Also eliminated a few minor glitches.

    o	The symbols() function is now implemented.

    o	New function termplot() with similar functionality to
	plot.gam() in S.

    o	The parameters to title() which specify the labels may now
	be specified as a list containing the parameter together
	with additional modifying par values (cex, col, font) which
	affect just that label.

	title() also has new line and outer arguments which provide
	functionality which matches that in axis().

    o	New functions which.min() amd which.max().

    o	The Wilcoxon and Ansari-Bradley tests now optionally return
	confidence intervals for the location or scale parameter of
	interest.

    o	New argument `extend' to window() (and updated documentation).

    o	write.table() can now write CSV files in the format Excel expects.

    o	New device xfig() to produce XFig files.

    o	New xyz.coords() utility function to be used for 3D highlevel plots.


    o	R CMD build now also works for package bundles.

    o	Rdconv allows an output file to be specified.

    o	Initial support for C++ source code in add-on packages under Unix.

    o	Mathlib can be built as a standalone library: see directory
	src/nmath/standalone.



BUG FIXES

    o	The Mathlib functions now use exactly the same values for
	+/-Inf, NaN and NA as the rest of R in all cases.

    o	Improved automatic remaking.


    o	option keep.source was not set correctly before the base
	package was loaded: some functions in the base package had
	the source kept.  The memory usage should now be reduced by ca 1Mb.

    o	The base file is no longer closed twice in case of a syntax
	error (caused segfault on Linux).

    o	The X11 data editor scrolls cells and so allows more than ca 10
	characters to be entered.  Several interface/redraw errors
	have been corrected.

    o	Using `destroy' or `close' on the X11 data editor window killed R.

    o	Multiple `destroy' events or X11 errors killed R (PR#400).

    o	Warnings from .Last or closing devices are printed where
	sensible (e.g. not on GNOME nor Windows console).

    o	add1.glm() and drop1.glm() gave incorrect results in the "Chisq"
	test option when the scale was estimated.

    o	aggregate() applied to multiple time series lost the series names.

    o	as.hclust.twins() in package mva sets method=NA (PR#538)

    o	ave(1:3) now works (as when is.null(list()) was TRUE years ago).

    o	barplot(c(0.1, 0.5, 1), ylim = c(0, 1)) now works: [xy]axs="i"
	and exact limits now labels the limits.

    o	by() works when embedded in a function.

    o	The xlab and ylab in coplot() now set the x and y axis labels,
	as in S.  Supply a second component to label the conditioning
	variables.

    o	count.fields() and read.table() now have the same default
	quote = "\"'".

    o	guard against segfault in dataentry(x<-1, Modes = plot), and the like.

    o	dev.print() now checks if the current device is replayable
	(and not all devices were, despite the documentation).

    o	The gtk() device (formerly x11() under GNOME) was incorrectly
	returning character information, so in particular `*' was
	wrongly centred as a plotting symbol.

    o	is.qr() checks not only for $qr, but also for $rank & $qraux, PR#482.

    o	library() will not leave the package on the search path if
	loading fails (including if .First.lib fails).

    o	lqs(, method="S") rounded k0 on passing to C.

    o	na.omit() now handles vectors and matrices as well as data
	frames.

    o	plot.lm(*, which=4) now works thanks to Marcel Wolbers.

    o	postscript() now uses the options "papersize" and "printcmd"
	rather than the values of R_PAPERSIZE in the environment
	and R_PRINTCMD found at build time.

    o	postscript() now makes use of kerning information in computing
	string widths.

    o	M <- 2 ; print(ppr(.., nterms = M))  now works.

    o	ppr(, sm.method="spline") had an internal limit of 250 rows:
	this is now 2500 and is now checked.

    o	predict.lm(,type="terms",se.fit=T) gives correct standard errors
	(thanks to John Maindonald)

    o	print.ftable() now returns its argument.

    o	proj.aovlist() now gives a non-zero result for strata with
	no fitted effects.

    o	qnorm() is now based on AS 241 instead of AS 111, and should
	give precise results up to 16 digits precision.

    o	rgeom(, prob=1) gives 0 rather than NA

    o	rpois(*, lambda) now works when lambda > .Machine$integer.max

    o	strheight("X") with no active device would segfault.

    o	system() is now (partially) functional on systems without popen.

    o	Fixed bug in undoc() - requiring new `chdir' argument
	for sys.source()

    o	Fixed problem in usemethod() where CAR(call) could be non-symbol.

    o	The x11() device no longer crashes R if a font is not found,
	and will warn if there is a size mismatch of more than 10%.


    o	R CMD Rd2dvi now sorts files alphabetically.

    o	Rdconv now reports if an invalid type is specified (rather
	than using latex).

    o	Support for Rd conversion to Sd has been reinstated (it was
	unintentionally removed along with nroff-based conversion to text).

    o	\deqn{} fix in R-exts.texi, PR#523.


    o	Linpack.h now makes clear which routines are actually in R.

    o	Entry-point "pythag" is now loaded even though it is not
	necessarily used in R.	Where "hypot" is available pythag
	just calls hypot after checking for special values.

    o	call_R will now correctly handle character vector arguments.

    o	The alphabet links on top of HTML function indices with more than
	100 entries now contain only the letters which are really
	first letters of at least one entry.



		CHANGES IN R VERSION 1.0.1


BUG FIXES

    o	pgamma(Inf, 1, Inf) gives NaN instead of an infinite loop, PR#462.

    o	Inline xaxt and yaxt parameters were ignored.

    o	Setting the normal RNG was not always recorded in .Random.seed.

    o	\link[pkg]{foo} links were wrongly translated to HTML.

    o	Direct use of show.data() with no args was incorrect.

    o	print.coefmat does sensible things if options
	show.signif.stars and show.coef.Pvalues are not set correctly.

    o	x <- list(a=1, b=2) ; x["c"] <- 3 now (again) stretches the list
	rather than give a "subscript out of bounds" error.

    o	Models with response appearing on rhs could cause segfault.

    o	as.data.frame.matrix will now ensure the columns added have
	non-empty names.

    o	Some (strange?) model formulas could cause memory corruption
	(thanks to John Fox for digging this up).

    o	Matrix multiplication in cases such as 1:3 %*% t(1:2) is accepted.

    o	Options --nsize and --vsize to R CMD check gave warning
	messages and only one was accepted.

    o	The autoload()s during startup are "wrapped" such
	that conflicting objects don't break startup.

    o	cor.test(*, meth="spear") {pkg ctest} now works (again) for n <= 6

    o	scale = 0 in biplot.princomp() now works.

    o	The scores given by princomp(, cor = TRUE) and the rotated
	values given by prcomp(, scale = TRUE) are now computed from the
	scaled data.

    o	barplot now works okay when length(col) < length(legend.txt),
	thanks to Ben Bolker, PR#494.

    o	legend has new args `ncol' and `horiz' thanks to Ben Bolker.

    o	kernel("dirichlet", m=10, r=1) in package ts now works.

    o	save/restore of	 environments containing "..." object should
	work now.

    o	qhyper should work better for large N.

    o	qbinom(1-1e-16, n, p) , qpois() and qnbinom(*) looped for ever.

    o	as.matrix.data.frame no longer escapes quotes in character
	vectors.

    o	R would try to save the readline history at the end of
	non-interactive sessions, causing crashes on some systems.

    o	Subtle roundoff problems caused arrays to be allocated short in
	loess.c in some cases, leading to segfaults.

    o	Document that postscript(file="") sends the output directly to
	the default printer.

    o	ts.union(, dframe=TRUE) had a long-standing typo, now works.

    o	save(, ascii=TRUE) had problem with octal escapes in strings
	when there was a digit following, should work now.

    o	matpoints() and matlines() now also have a "type =" argument
	with defaults "p" and "l", respectively; PR#506.

    o	The new Perl 5.6 broke our version-detection mechanism. A
	better one has been inserted.

    o	X11(colortype="gray") failed to work on 8-bit screens, and
	more generally when colour allocation failed X11() did not
	revert to monochrome correctly (and did not say it was doing so).

	It was not documented in the help that to change the X11
	colortype one needs to close all open X11 devices.

    o	loessf.f in modreg defined DSIGN unecessarily and this caused
	a conflict on AIX.

    o	plot.lm will now work with rlm objects.

    o	start and end behave better when the frequency is not an integer.

    o	aggregate.ts is closer to S-PLUS's aggregate.rts.

    o	quantile(x) now works when x contains several +/- Inf's.

    o	guard against segfault in dataentry(0,0) (or, more
	realistically, when mistyping data.entry(x,y) as
	dataentry(x,y))


	*********************************************************
	*							*
	*	News of 1.0.0 and earlier is in file `ONEWS'	*
	*							*
	*********************************************************
