[R] R 2.13.1 is released
Peter Dalgaard
pd.mes at cbs.dk
Fri Jul 8 12:16:40 CEST 2011
I've rolled up R-2.13.1.tar.gz a short while ago. This is a maintenance release to consolidate various minor fixes to 2.13.0.
The Licencing change to GPL-2 | GPL-3 may be of interest to some.
You can get it from
http://cran.r-project.org/src/base/R-2/R-2.13.1.tar.gz
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:
MD5 (AUTHORS) = ac9746b4845ae866661f51cfc99262f5
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = a6f58169fec241d4fa4ab283d8cb12de
MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331
MD5 (NEWS) = 8347135398220ba817bbf1c97586ec53
MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71
MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db
MD5 (R-latest.tar.gz) = 28dd0d68ac3a0eab93fe7035565a1c30
MD5 (README) = 296871fcf14f49787910c57b92655c76
MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da
MD5 (THANKS) = 03d783ff71270c77d497fd573d711fd8
MD5 (R-2/R-2.13.1.tar.gz) = 28dd0d68ac3a0eab93fe7035565a1c30
This is the relevant part of the NEWS file:
R News
CHANGES IN R VERSION 2.13.1:
NEW FEATURES:
• iconv() no longer translates NA strings as "NA".
• persp(box = TRUE) now warns if the surface extends outside the
box (since occlusion for the box and axes is computed assuming
the box is a bounding box). (PR#202.)
• RShowDoc() can now display the licences shipped with R, e.g.
RShowDoc("GPL-3").
• New wrapper function showNonASCIIfile() in package tools.
• nobs() now has a "mle" method in package stats4.
• trace() now deals correctly with S4 reference classes and
corresponding reference methods (e.g., $trace()) have been added.
• xz has been updated to 5.0.3 (very minor bugfix release).
• tools::compactPDF() gets more compression (usually a little,
sometimes a lot) by using the compressed object streams of PDF
1.5.
• cairo_ps(onefile = TRUE) generates encapsulated EPS on platforms
with cairo >= 1.6.
• Binary reads (e.g. by readChar() and readBin()) are now supported
on clipboard connections. (Wish of PR#14593.)
• as.POSIXlt.factor() now passes ... to the character method
(suggestion of Joshua Ulrich). [Intended for R 2.13.0 but
accidentally removed before release.]
• vector() and its wrappers such as integer() and double() now warn
if called with a length argument of more than one element. This
helps track down user errors such as calling double(x) instead of
as.double(x).
INSTALLATION:
• Building the vignette PDFs in packages grid and utils is now part
of running make from an SVN checkout on a Unix-alike: a separate
make vignettes step is no longer required.
These vignettes are now made with keep.source = TRUE and hence
will be laid out differently.
• make install-strip failed under some configuration options.
• Packages can customize non-standard installation of compiled code
via a src/install.libs.R script. This allows packages that have
architecture-specific binaries (beyond the package's shared
objects/DLLs) to be installed in a multi-architecture setting.
SWEAVE & VIGNETTES:
• Sweave() and Stangle() gain an encoding argument to specify the
encoding of the vignette sources if the latter do not contain a
\usepackage[]{inputenc} statement specifying a single input
encoding.
• There is a new Sweave option figs.only = TRUE to run each figure
chunk only for each selected graphics device, and not first using
the default graphics device. This will become the default in R
2.14.0.
• Sweave custom graphics devices can have a custom function
foo.off() to shut them down.
• Warnings are issued when non-portable filenames are found for
graphics files (and chunks if split = TRUE). Portable names are
regarded as alphanumeric plus hyphen, underscore, plus and hash
(periods cause problems with recognizing file extensions).
• The Rtangle() driver has a new option show.line.nos which is by
default false; if true it annotates code chunks with a comment
giving the line number of the first line in the sources (the
behaviour of R >= 2.12.0).
• Package installation tangles the vignette sources: this step now
converts the vignette sources from the vignette/package encoding
to the current encoding, and records the encoding (if not ASCII)
in a comment line at the top of the installed .R file.
LICENCE:
• No parts of R are now licensed solely under GPL-2. The licences
for packages rpart and survival have been changed, which means
that the licence terms for R as distributed are GPL-2 | GPL-3.
DEPRECATED AND DEFUNCT:
• The internal functions .readRDS() and .saveRDS() are now
deprecated in favour of the public functions readRDS() and
saveRDS() introduced in R 2.13.0.
• Switching off lazy-loading of code _via_ the LazyLoad field of
the DESCRIPTION file is now deprecated. In future all packages
will be lazy-loaded.
• The off-line help() types "postscript" and "ps" are deprecated.
UTILITIES:
• R CMD check on a multi-architecture installation now skips the
user's .Renviron file for the architecture-specific tests (which
do read the architecture-specific Renviron.site files). This is
consistent with single-architecture checks, which use
--no-environ.
• R CMD build now looks for DESCRIPTION fields BuildResaveData and
BuildKeepEmpty for per-package overrides. See ‘Writing R
Extensions’.
BUG FIXES:
• plot.lm(which = 5) was intended to order factor levels in
increasing order of mean standardized residual. It ordered the
factor labels correctly, but could plot the wrong group of
residuals against the label. (PR#14545)
• mosaicplot() could clip the factor labels, and could overlap them
with the cells if a non-default value of cex.axis was used.
(Related to PR#14550.)
• dataframe[[row,col]] now dispatches on [[ methods for the
selected column (spotted by Bill Dunlap).
• sort.int() would strip the class of an object, but leave its
object bit set. (Reported by Bill Dunlap.)
• pbirthday() and qbirthday() did not implement the algorithm
exactly as given in their reference and so were unnecessarily
inaccurate.
pbirthday() now solves the approximate formula analytically
rather than using uniroot() on a discontinuous function.
The description of the problem was inaccurate: the probability is
a tail probablity (‘2 _or more_ people share a birthday’)
• Complex arithmetic sometimes warned incorrectly about producing
NAs when there were NaNs in the input.
• seek(origin = "current") incorrectly reported it was not
implemented for a gzfile() connection.
• c(), unlist(), cbind() and rbind() could silently overflow the
maximum vector length and cause a segfault. (PR#14571)
• The fonts argument to X11(type = "Xlib") was being ignored.
• Reading (e.g. with readBin()) from a raw connection was not
advancing the pointer, so successive reads would read the same
value. (Spotted by Bill Dunlap.)
• Parsed text containing embedded newlines was printed incorrectly
by as.character.srcref(). (Reported by Hadley Wickham.)
• decompose() used with a series of a non-integer number of periods
returned a seasonal component shorter than the original series.
(Reported by Rob Hyndman.)
• fields = list() failed for setRefClass(). (Reported by Michael
Lawrence.)
• Reference classes could not redefine an inherited field which had
class "ANY". (Reported by Janko Thyson.)
• Methods that override previously loaded versions will now be
installed and called. (Reported by Iago Mosqueira.)
• addmargins() called numeric(apos) rather than
numeric(length(apos)).
• The HTML help search sometimes produced bad links. (PR#14608)
• Command completion will no longer be broken if tail.default() is
redefined by the user. (Problem reported by Henrik Bengtsson.)
• LaTeX rendering of markup in titles of help pages has been
improved; in particular, \eqn{} may be used there.
• isClass() used its own namespace as the default of the where
argument inadvertently.
• Rd conversion to latex mis-handled multi-line titles (including
cases where there was a blank line in the \title section).
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
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