[R] R 1.9.1 is released

[Peter Dalgaard]

I've rolled up R-1.9.1.tgz a short while ago. This is a maintenance
version mainly to fix a number of minor bugs and issues (the most
annoying one seems to have been the change to barplots of tables) and
some installation issues.

Because of the relocation the CVS archives, there is no direct access
to the files until they show up on the CRAN master site. You can then
get it from

http://cran.r-project.org/src/base/R-1.9.1.tgz

or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.
 
There is also a version split for floppies.

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

c8201425506e5c077ef1936e19ea2f51  R-1.9.1.tgz
7683777a649e099d9c278ebc58fcbc56  R-1.9.1.tgz-split.aa
c0b8dba896ab7cf1fd2e597f400bfe07  R-1.9.1.tgz-split.ab
ded2cc8335f338f80cf5380d6394f7ab  R-1.9.1.tgz-split.ac
1d35502fdf6876e71e5218603a47394d  R-1.9.1.tgz-split.ad
51a7cfa9effcd9e61fbb44ee78a86de9  R-1.9.1.tgz-split.ae
5419f461683e8c98cd8cfaa308df0b40  R-1.9.1.tgz-split.af
183e16b38224b3c6c39b400aaa6172a0  R-1.9.1.tgz-split.ag


        For the R Core Team
        Peter Dalgaard



Here's the relevant bit of the NEWS file:


		CHANGES IN R VERSION 1.9.1


NEW FEATURES

    o	as.Date() now has a method for "POSIXlt" objects.

    o	mean() has a method for "difftime" objects and so summary()
	works for such objects.

    o	legend() has a new argument 'pt.cex'.

    o	plot.ts() has more arguments, particularly 'yax.flip'.

    o	heatmap() has a new 'keep.dendro' argument.

    o	The default barplot method now handles vectors and 1-d arrays
	(e.g., obtained by table()) the same, and uses grey instead of
	heat color palettes in these cases.  (Also fixes PR#6776.)

    o	nls() now looks for variables and functions in its formula in
	the environment of the formula before the search path, in the
	same way lm() etc look for variables in their formulae.


INSTALLATION ISSUES

    o	src/modules/X11/dataentry.c would not build on some XFree
	4.4.0 systems.	(This is a bug in their header files but we have
	added a workaround.)

    o	Building with gcc/g77 3.4.0 on ix86 platforms failed to produce
	a working build: the critical LAPACK routines are now compiled
	with -ffloat-store.

    o	Added patches to enable 64-bit builds on AIX 5.1: see the R-admin
	manual for details.

    o	Added some patches to allow non-IEEE-754 installations to work
	reasonably well.  (Infs and NAs are still not handled properly
	in complex arithmetic and functions such as sin().  See also
	Deprecated, as support for non-IEEE-754 installations is about
	to be removed.)

    o	Installation will now work in Estonian (et_EE*) locales, which
	sort z before u.  (PR#6958)


DEPRECATED & DEFUNCT

    o	Support for non-IEEE-754 arithmetic (which has been untested
	for some time) will be removed in the next full release.

    o	Direct use of R INSTALL|REMOVE|BATCH|COMPILE|SHLIB is
	deprecated: use R CMD instead.

    o	The gnome/GNOME graphics device is deprecated and will be
	removed in the next full release.


BUG FIXES

    o	pbinom(q, N, prob) is now more accurate when prob is close to 0.
	(PR#6757)

    o	pcauchy(x, .., log.p) is now more accurate for large x,
	particularly when log.p = TRUE. (PR#6756)

    o	pgeom(q, prob, lower.tail, log.p) is now (sometimes much) more
	accurate when prob is very small. (PR#6792)

	The code for pgeom(prob=1) assumed IEEE 754 arithmetic, and
	gave NaNs under gcc 3.4.0 -fPIC, for example.

    o	makeARIMA() was not handling an ARMA(0, 0) model correctly.

    o	as.Date() was failing on factors.  (PR#6779)

    o	min(), max() and range() were failing on "difftime" objects.

    o	as.data.frame.list() could fail on some unusual list names.
	(PR#6782)

    o	type.convert() ignored na.strings when no conversion was done.
	(PR#6781, not needed for its primary use in read.table.)

    o	Fixed a clipping problem in the quartz() device.

    o	Subsetting a factor swapped the order of the attributes, which
	identical() cares about.  (PR#6799)

    o	The L-BFGS-B option of optim() apparently needs part of its
	workspace zeroed.  (PR#6720)

    o	extractAIC.survreg() needed updating.

    o	When using the header Rmath.h in standalone mode, the case where
	TRUE, FALSE are already defined is now handled correctly.

    o	Package utils now exports several functions that are needed for
	writing Sweave drivers.

    o	Comparison of two lists/expressions was giving nonsensical
	(and often random) answers, and is now an error.

    o	The C-level function ncols was returning a random answer
	(often 0) for a 1D array.  This caused model.matrix to
	misbehave (perhaps segfault) if a term was a 1D array.	(PR#6838)

    o	The configure script now finds the pdf viewers ggv and gpdf.

    o	Workaround for the problems strptime on MacOS X has with dates
	before 1900.

    o	'R CMD build' works in a directory whose path contains spaces.
	(PR#6830 under Unix/Linux: it already worked under Windows.)
	Also 'R CMD check'.

    o	mosaicplot() stops cleanly if given a table containing missing values.

    o	install.packages() from a local CRAN was broken.

    o	bxp() fixed for e.g.,  boxplot(..., border=2:4)

    o	approx(list(x=rep(NaN,9), y=1:9), xout=NaN) does not seg.fault
	anymore (PR#6809).

    o	plot(1, pch=NA) does not give an error anymore and
	plot(1:2, pch=c("o",NA)) only prints one symbol	 (PR#6876).

    o	diffinv(matrix(3, 7,0)) now works.

    o	plot.ts(z) for multivariate 'z' now properly draws all 'nc' xlab`s
	when nc > 1 and obeys 'ann=FALSE' or 'axes=FALSE'.

    o	aggregate(.data.frame) failed if the answer would have had one
	row.

    o	recordPlot() and replayPlot() failed to duplicate the display
	list, so further plotting altered the saved or replayed object.

    o	Assignments of the form adf[i,j] <- value now accept a
	data-frame value as well as a list value.

    o	dir.create() sometimes erroneously continued to report a directory
	already existed after the first instance.  (PR#6892)

    o	arima.sim() allows a null model.

    o	which.min() & which.max()'s C code now PROTECT()'s its result.

    o	Building standalone nmath did not support some of the DEBUG options.

    o   mle() got confused if start value list was not in same order as
        arguments of likelihood function (reported by Ben Bolker)

    o	backsolve(r, x, k) now allows k < nrow(x) - as its documentation
	always claimed.

    o	update.packages("mgcv") and old.packages(*) now give a better error
	message; and installed.packages("mgcv") properly returns <empty>.

    o	stats:::as.dendrogram.hclust() is documented and no longer re-sorts
	the two children at each node.	This fixes as.dendrogram(hh) for
	the case where hh is a "reordered" hclust object.

	plot.dendrogram(x) now draws leaves 'x' more sensibly.

	reorder.dendrogram() now results in a dendrogram with correct
	"midpoint"s, and hence reordered dendrograms are plotted correctly.

	stats:::midcache.dendrogram() and hence the reorder() and rev()
	dendrogram methods do not return bloated dendrograms.

    o	heatmap(*, labRow=., labCol=.) now also reorders the labels when
	specified---not only when using default labels.

    o   Copying lattice (grid) output to another device now works again
        (There were intermittent problems in 1.9.0 - PR#6915, #6947/8.)

    o	hist() uses a more robust choice of its 'diddle' factor, used
	to detect if an observation is on a bin boundary.  (PR#6931)

    o	jitter(x) now returns x when length(x) == 0.

    o	Under some rare circumstances the locale-specific tables used by
	the perl=TRUE option to grep() etc were being corrupted and so
	matches were missed.

    o	qbinom(*, prob = 0, lower.tail = FALSE) now properly gives 0.
	(PR#6972)

    o	Class "octmode" needed a "[" method to preserve the class: see
	example(file.info) for an example.


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

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