R 2.13.1 is released

From: Peter Dalgaard <pd.mes_at_cbs.dk>
Date: Fri, 08 Jul 2011 12:16:40 +0200

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


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.

    • 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

    • 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

    • 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

    • 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

    • R CMD build now looks for DESCRIPTION fields BuildResaveData and
      BuildKeepEmpty for per-package overrides.  See ‘Writing R

  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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