[R] R 2.8.1 is released

Peter Dalgaard p.dalgaard at biostat.ku.dk
Mon Dec 22 10:24:27 CET 2008

I've rolled up R-2.8.1.tar.gz a short while ago.

This is a maintenance release and fixes a number of mostly minor bugs
and platform issues.

See the full list of changes below.

You can get it (in a short while) from


or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.

         For the R Core Team

         Peter Dalgaard

These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:

70447ae7f2c35233d3065b004aa4f331  INSTALL
433182754c05c2cf7a04ad0da474a1d0  README
4f004de59e24a52d0f500063b4603bcb  OONEWS
ff4bd9073ef440b1eb43b1428ce96872  ONEWS
4eff8b4937a55a2c3ece8b0a31772b62  NEWS
1ad28cbc84485ccdf4ce5721b34ed645  THANKS
070cca21d9f8a6af15f992edb47a24d5  AUTHORS
a6f89e2100d9b6cdffcea4f398e37343  COPYING.LIB
eb723b61539feef013de476e68b5c50a  COPYING
020479f381d5f9038dcb18708997f5da  RESOURCES
5d443029346cbad2f2df7c62a0ea8e0f  FAQ
acd40621b8942a2464daa2f9cef3273d  R-2.8.1.tar.gz
acd40621b8942a2464daa2f9cef3273d  R-latest.tar.gz

Here is the relevant part of the NEWS file:



     o	sum() now has a method for "difftime" objects (via the Summary

	max(), min() and range() applied to "difftime" object(s) now
	return a result in the common units of the objects, if there
	is one.

     o	installed.packages() is now tolerant of malformed DESCRIPTION
	files in installed packages (it ignores them, with a warning).

     o	qt() now works for 0 < df < 1.

     o	For consistency with matrix() and array(), dimnames(x) <-
	list() removes the dimnames (as assigning NULL would do).
	It was previously an error.

     o	nlminb() copies names from 'start' to the parameter vector
	used (for consistency with optim()).

     o	legend() gains a 'title.col' argument: the title colour was
	previously set from the first element of 'text.col' (which
	remains the default).

     o	In an Rd file, use of top-level \itemize{} inside a \value{}
	block is unnecessary and almost always gave a faulty
	conversion.  Most cases are now detected and corrected, but
	give a warning as such code will not work correctly in earlier
	versins of R.

	Also, use of \code{} inside a code block such as \examples{}
	will give a erroneous conversion that is now detected and
	warned against.

     o	Autoflushing of stdout is turned on when Rd processing, so
	warnings/error are likely to appear in the right place in
	redirected output (such as that from R CMD check).


     o	R_PDFLATEXCMD is added to the environment variables set by
     	'R CMD' and is used by R CMD Rd2dvi.

	default to 'latex', 'pdflatex', 'makeindex' and 'dvips'
	respectively if no suitable executable was found at configure
	time (since they might well be available at run time,
	particularly for binary installations of R).  This affects
	R CMD Rd2dvi and help(offline=TRUE).

	R CMD Rd2dvi now gives an explicit error message if latex (or
	pdflatex) fails.

	R CMD Rd2dvi gains a --no-index argument: processing some
	special characters on PDF indices gave errors which used to be


     o	R CMD INSTALL --with-package-versions is deprecated (and
	support has always been incomplete on Windows).

	So is install.packages(installWithVers = TRUE).

     o	Rd conversion to Sd and Ssgm is now deprecated as we no longer
	have any means to check the results (and Sd is long obsolete).


     o	add1.glm() no longer warns if applied to a binomial glm with a
	factor response.

     o	aggregate.data.frame() now does something sensible with a
	zero-column 'x' rather than failing with an obscure error
	message.  It gives an explicit error message if called with a
	zero-row 'x'.

     o	integrate() now accepts integer results from f(): as documented,
	but only double was accepted.

     o	contrib.url() produced an incorrect URL for the type

     o   pairwise.wilcox.test() did not pass on the 'paired' argument
         (caught by Matthias Kohl)

     o	bmp(), jpeg(), and png() on unix with type="cairo" would segfault
	on closure if the output file could not be opened.

     o	tiff() on unix would not write the output file for the first page
	when multiple pages were plotted.

     o   str(1 + structure(1, class = "test")) no longer recurses 

     o	pf(x, .., ncp, lower.tail=FALSE, log=TRUE) is much more accurate
	for large x now.

     o	dev2bitmap() failed in 2.8.0 if 'taa' and 'gaa' were both NA.

     o	Under rare circumstances equality tests for character strings
     	could fail to report equality in 2.8.0 in the same way as
     	2.7.2.  (This needed a current encoding of Latin-1 or UTF-8,
     	one string whose encoding was marked as that encoding and one
     	that was marked as "unknown".  In that circumstance the two
     	strings are not actually known to be equal, but earlier
     	versions of R assumed that "unknown" meant the current
     	encoding, and this is done once again.)

     o	R CMD config could echo messages from GNU make if called from
	within a Makefile (as e.g. package Rcpp did), especially from
	within a parallel make run.

     o	Rounding error could affect window(extend=TRUE) when applied
	to monthly series.  (PR#13272)

     o	Offline help on a Unix-alike now works even if options
	"latexcmd" and "dvipscmd" contain spaces
	(e.g. "dvips -Pmy_printer").

	Informative error messages are given if running latex or dvips

     o	Using plot.lm() on a "glm" object since 2.7.1 with which=5
	caused the Pearson rather than deviance residuals to be used
	in which=2 or 3 (including in the default case).  (Thanks to
	Effie Greathouse and Greg Snow.)

	plot.lm() did not report on omitting observations with
	leverage one if they also had residual exactly zero.  This was
	seen in example(occupationalStatus).

     o	deparse(nlines=) no longer pads short results with blank
	lines. (PR#13299)

     o	legend(xpd=) now restores 'xpd' correctly.  (PR#12756)

     o	The "formula" method for lines() now works if 'subset' is
	supplied and no 'data' argument (as that for points() did).

     o	Sweave() now takes the defaults for the options 'pdf.version'
	and 'pdf.encoding' of its RweaveLatex driver from pdf.options().

     o	prettyNum(x, drop0trailing=TRUE) treated "1.1e20" as "1.1e2"
	and hence str() did as well, in 2.8.0 only.

     o	dchisq(x, df, ncp) no longer hangs for large x and ncp > 0,
	and is more accurate in some cases (PR#13309).

     o	installed.packages(lib.loc = D, priority="NA") now also works when
	D contains a single package.  (PR#13332)

     o	legend(...., merge=TRUE) now warns and has no effect in the
	case where no line segments are drawn.  (PR#13340)

     o 	transform.data.frame() works better when two or more columns are

     o	Deparsing argument lists with non-syntactic names (e.g. that for
	transform()) now uses backticks rather than double quotes to
	produce syntactically valid output.

     o	matrix() failed to check for 0-length 'dimnames': it now
	treats them as NULL (as array did).  (PR#13361)

     o	0^NA is now NA, not Inf, consistent with x^NA, x != 1.

     o	anova.mlm() did not work if T had only one row (including
	e.g. the case M = ~1).

     o	axis.POSIXct() mislabelled for some time ranges of a few hours
	(reported by Martin Becker).

     o	mantelhaen.test() with 'exact=FALSE' was not respecting
	'alternative'. It now does one-sided tests similarly to

     o	anova.mlm() had trouble with some designs where near-zero rows of
	the tranformation matrix were not removed (caught by Nils Skutara).

     o	Rd conversion was handling expressions like
	'\item{foo}{see \eqn{x}}' (with one argument to \eqn
	immediately followed by a right brace) incorrectly, sometimes
	giving a spurious warning about 'missing text'.

     o	R CMD INSTALL used the C locale to install the DESCRIPTION
	file, and so escaped non-ASCII characters in packages with a
	declared encoding of "latin1" or "UTF-8".  (However, the
	installed DESCRIPTION file was rarely used since the dumped
	metadata are available.)

     o	xspline() now respects inline par settings.

	It and grid.xspline() now handle the special case of only two
	control points, and splines with control points that are
	located well outside the device (e.g., a zoomed view of a
	larger curve).	(Both cases were giving the error "reached

     o	In setClass("C", contains="list"); x <- new("C", 1:3), x[2:3] now
         remains of class "C".  So does rep(x, 2) or rep.int(x, 3).

     o	median.default() now also works for "numeric"-like vectors.

     o	The pdf() device can now handle the case where an image uses a
	very large number of colours with different levels of
	semi-transparency (alpha-values).  It used to segfault.
	(Also PR#13264.)

     o	window() failed to apply a fuzz to 'start' or 'end' and so
	sometimes warned incorrectly for time series with 'freq' not a
	power of two (e.g. 12 or 24).

     o	unique.default() now preserves the "tzone" attribute on
	"POSIXct" objects.

     o	If all the packages had dependency lists of equal lengths,
	occasionally install.packages() would compute an incorrect
	sort order.

     o	col(x, as.factor=TRUE) and row(x, as.factor=TRUE) would fail
	if x had no column (row) names.  It was documented
	incorrectly, and now returns a matrix factor.

     o	setRepositories() failed if "pkgType" was set to

     o	formals<-() changed the body of the function if this was a
     	length-one list.

     o	body<-() failed if the function had no arguments.  It now
	warns if discarding elements from a 'value' of type "expression".

     o	qr.coef() failed in the complex case for non-square systems.

     o	plot.dendrogram(horizontal=TRUE) did not not plot 'edgetext'
	at the correct locations.  (PR#13313)

     o	The starting point for plot.acf(ci.type="ma") was lag 0 when it
	should have been lag 1.  (PR#13071)

     o   There was an obscure bug with srcrefs, which could put the
         parser into a condition giving "Error: bad value" on any input

    O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
   c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
  (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)              FAX: (+45) 35327907

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