R-beta: R-0.62 is released

Peter Dalgaard BSA (p.dalgaard@biostat.ku.dk)
14 Jun 1998 16:42:30 +0200

To: R-announce@stat.math.ethz.ch
Subject: R-beta: R-0.62 is released
From: Peter Dalgaard BSA <p.dalgaard@biostat.ku.dk>
Date: 14 Jun 1998 16:42:30 +0200

I've put up R-0.62.0.tgz up for FTP from Auckland some minutes ago.
As usual, don't get it from there unless you are desperate, but wait
for it to be mirrored at a CRAN site near you within a day or two.

Note that beginning with this version, you need Fortran in some form
or other to compile R. (f2c is good enough)

Here is the relevant part of the CHANGES file:



    o   Many more help(.) pages.

    o   The top level Makefile now supports the usual
	   ./configure; make; make install
	procedure (new make targets `all' and `install').

    o   The HTML help pages can now be searched for keywords.

    o	Conversion of functions to and from lists. formals<- and body<-.
	The alist() function makes it easier to construct argument lists,
	etc. Added expression-->list coercion.

    o	complex(.) now has optional 'argument' and 'modulus' arguments,
	allowing ``polar coordinate'' specifications.

    o	layout() documented and improved: starts default device if needed, and
	returns number of figures.

    o	New find() function [relying on apropos(..)].

    o	objects(<integer>) now works, being equivalent to

    o	storage.mode() and related functions now return
	"double" instead of "real", for compatibility.
	"real" is still allowed as synomym for "double".

    o	A tests/ directory has been added (in the source), and "make tests"
	has been modified to run more than all the examples from the base
	package.  The exact 'make tests' behavior is still bound to change.

    o	An experimental directory etc/Rdoc has been added with a perl5
	module to parse R documentation files.	Sample perl programs
	to use this module are also included.

    o	All internal mechanisms to support factors and data.frames
	have been removed.  These are now entirely supported by
	interpreted code! `is.unordered' has been eliminated.
	Thanks to John Chambers for allowing the distribution of his
	StatLib code.

    o	"pmatch" is now completely S compatible and is not just another
	name for "charmatch".

    o	There is now a function called ".Alias" which can be used to
	provide multiple names for the same object.  Example:
		lm2 <- .Alias(lm)
	This is dangerous because it can be used to defeat the
	call-by-value illusion.

    o	Many functions changed from <primitive> to .Internal(..).
	Currently, new .Internal(.)s in ..library/base/R/New-Internal.R
	Primitive functions are now printed as ``.Primitive(..)''.

    o	[dpqr]hyper(.) now also work with some 0 arguments.

    o	C-code: Many "-Wall" fixes (MM & DB).

    o	mva's dist() now takes arguments diag and upper which control
	how the distance matrix is printed. plot.hclust() now takes a
	labels argument.

    o	Attributes are now propagated correctly in binary operations.
	Changes from:
	  Steve Oncley and Gordon Maclean
	  National Center for Atmospheric Research
	  Boulder, Colorado USA

    o	configure now also checks for fort77.

    o	Usage of R INSTALL now is
	  R INSTALL [options] [-l lib] pkg_1 ... pkg_n
	The +/- options were replaced by GNU-style `--no-docs' and
	`--no-text', `--no-html', and `--no-latex'.

    o	Usage of R REMOVE now is
	  R REMOVE [options] [-l lib] pkg_1 ... pkg_n

    o	Usage of R COMPILE now is R COMPILE [options] srcfiles, where
	through options one can set e.g. CFLAGS or FFLAGS.

    o	Usage of R SHLIB now is R SHLIB [-o libname] files, where the
	file names can be that of source or object files.

    o   A new R CMD interface allows invokation of executables in
	$RHOME/{etc,cmd} without installing them or setting paths.

    o	Data files are now also documented using the Rd format, all
	data documentation in the base package has been converted
	accordingly. Rd files for data have a \keyword{datasets} as

    o	new function mahalanobis() for Mahalanobis distance

    o	quantile.default() now handles Inf's correctly.

    o	New command line options `--enable-blas' and `--enable-readline'
	to configure.

    o	pretty(x) is more reasonable when max(x)-min(x) < 1e-10 max(|x|),
	and has a new argument "shrink.sml" for that case.

    o	formatC(.) supports a new "fg" format for flexible
	non-exponential formatting.

    o	etc/build-htmlpkglist has been integrated into etc/build-help
	(option --htmllists)

    o	family	gaussian(.) and inverse.gaussian(.) both accept several
	link arguments [J.Lindsey].

    o	The graphics function "tck" now produces effects just
	like those in S (e.g. par(tck=1) now produces grid lines).
	Since using "tck" produces nasty results in some circumstances
	there is also an alternative parameter "tcl" which defines
	the tick length in terms of lines of text.  The default
	setting is par(tcl=-0.5).

    o	menu() now takes additional arguments `graphics' (currently
	unused) and `title'.

    o	New function plot.formula().
	plot.factor() now produces boxplots when given 2 arguments.

    o	New function write.table().

    o	signif() now has a `digits' default of 6.

    o	Old-style long command line options (`-save' etc) changed to
	GNU-style (`--save' etc).
	Debugging options (`-ddd', `-gdb', `-xxgdb') unified into the
	new `--debugger' (`-d').
	New command line options `--version' (`-V') and `--help' (`-h')
	which print useful information and exit.

    o	The loading of profiles at startup now works as follows.
	Unless the new `--no-site-file' was given, a site profile is
	sought (as specified via the environment variable `RPROFILE',
	or if this is unset defaulting to `${RHOME}/etc/Rprofile'.
	Then, unless the new `--no-init-file' was given, the user
	profiles (`.Rprofile' and `~/.Rprofile') are sought.

    o	New functions subset() and transform() intended primarily to
	make life with dataframes easier.

    o	debian directory has been added so Debian GNU/Linux packages can be
	created from raw source.

    o	The graphics system has been through a major overhaul.
	It is now possible to have multiple active device drivers
	and to control them with full suite of dev.xxx() functions
	available in S.	 Display lists are now kept for interactive
	devices.  When an on-screen graphics window is resized,
	the content of that window is redrawn at the new size.
	At present only X11 and PostScript graphics device drivers
	are available, but more are on the way.

    o	On systems using IEEE arithmetic, the builtin Inf and NaN
	values are now recognised and used.  NA and NaN should
	propagate correctly in computations, with NA dominating
	in computations involving both quantities.
	E.g. NA+NaN is NA.

    o	Some of the t, F, and chisq distribution/probability functions
	now allow a noncentrality parameter `ncp'.

    o	Functions ptukey() and qtukey() provide the distribution and
	quantile functions for the maximum of several studentized

    o	system.file()  [now documented] returns all files matched by

    o	data() now supports more file formats: .RData for binary
	files, .txt or .tab for data to be read by
	`read.table(file, header=TRUE)' and .csv for data to be read
	by `read.table(file, header=TRUE, sep=";")'

    o	Rdconv: new tabular environment, new sections `\format' and
	`\source', new output format `-type Sd' for S documentation

    o	.First.lib() now implemented; called by library() after loading
	a package.

    o	print.summary.[g]lm() now give `significance stars' and a symbolic
	correlation matrix.

    o	new is.R() function.

    o	glm() now also returns an AIC value [from JL].
	print..glm methods indicate the options()$contrasts in some cases.
	In summary.glm(..., correlation=..), the default has been changed to
	corr. = FALSE  which is consistent with	 summary.lm().
	predict() now works again for glm objects.

    o	the `flag' argument in formatC(.) can now have more than one

    o	nlm() returns the number of iterations used [from J.Lindsey].

    o	cut, diff, hist, mean, quantile, seq, trunc()  are now all generic.
	cut() has an `include.lowest' argument as S.

    o	save.image() as short-cut to save the current session in .RData.

    o	new design of HTML help pages, including an index of all
	functions from all installed packages.

    o	new editor function pico()

    o	matrices and arrays can have zero extents

BUG FIXES (many of which resulted from the added features...)

    o	atanh(.) now works

    o   summary(glm) and summary(lm) now use compatible names.

    o   [pq]tukey(.) now working.

    o	title() now handles main=, sub=, xlab=, ylab= with embedded
	newlines correctly.  This is partly a change in title and
	partly a change in the underlying graphics code.

    o	min(.), max(.), sum(.)	now return integer for integer arguments.

    o	which(.) now returns integer.

    o	Rd files: leading whitespace of lines in user-defined sections
	was not correctly removed by Rdconv

    o	sign(.) works again.

    o	[.data.frame segfaulted if arg. wasn't a data frame

    o	"R --no-readline" now again gives proper prompts.

    o	demos/zero.R  dyn.load(.) now should be working more easily.

    o	mode(.) now returns "(" for a "parentheses 'call'".

    o	Bug fix in mva dist.c for method binary (gave "invalid
	distance"). plot.hclust failed for data without row names.

    o	R INSTALL should work (again) now when `pkg' is a relative file

    o	.not.yet.implemented() now takes an arbitrary number of args.

    o	Plotting of dendrograms is working again.

    o	data.frame(.) now uses "1:n" as default row.names.

    o	image(.) and contour(.) now also work called as, e.g., ``image(z)''.

    o	the first argument of axis(.) is now called `side' as in S.

    o	format(NULL) now works.

    o	minor fix in symnum.

    o	hist() now is more compatible to S, has a new `labels' argument,
	and should work ok for non-equidistant breaks.

    o	plot(-1) now labels properly.

    o	Many small code changes (eliminating extraneous variables, nested comm.)
	in C code in order to satisfy `gcc -Wall' [Doug Bates].

    o	model.extract() will now extract arbitrary model frame arguments.

    o	list of currently loaded libraries (.Dyn.libs) not saved
	from session to session (really, this time)

    o	rhyper works with vectorisation, degenerate cases.

    o   printing of objects in lists now dispatches methods correctly

   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)             FAX: (+45) 35327907
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