[R] R 2.12.1 is released

From: Peter Dalgaard <pd.mes_at_cbs.dk>
Date: Thu, 16 Dec 2010 10:35:01 +0100

I've rolled up R-2.12.1.tar.gz a short while ago. This is an update release, which fixes a number of mostly minor issues, and some consolidation within the area of reference classes. The most serious issues were probably that we were not catching misspelled NAMESPACE directives and not catching accidentally unnamed switch() arguments (notice that fixing either will likely uncover errors in preexisting code)

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) = 49b596b26b3e5c082dfde8bacfdffcb0
MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331
MD5 (NEWS) = 453317871e758763aa9bf385b545bdc6
MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71
MD5 (OONEWS) = 58d5b3b614888a6e366ff0c60073584f
MD5 (R-latest.tar.gz) = 078e8d1179fc9a762e326e6da2725468
MD5 (README) = 296871fcf14f49787910c57b92655c76
MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da
MD5 (THANKS) = f2ccf22f3e20ebaa86f8ee5cc6b0f655
MD5 (R-2/R-2.12.1.tar.gz) = 078e8d1179fc9a762e326e6da2725468

This is the relevant part of the NEWS file:

R News

CHANGES IN R VERSION 2.12.1:   NEW FEATURES:      The DVI/PDF reference manual now includes the help pages for all

      the standard packages: splines, stats4 and tcltk were previously
      omitted (intentionally).

     <URL: http://www.rforge.net> has been added to the default set of
      repositories known to setRepositories().

     xz-utils has been updated to version 5.0.0.

     reshape() now makes use of sep when forming names during       reshaping to wide format. (PR#14435)

     legend() allows the length of lines to be set by the end user       _via_ the new argument seg.len.

     New reference class utility methods copy(), field(),       getRefClass() and getClass() have been added.

     When a character value is used for the EXPR argument in switch(),

      a warning is given if more than one unnamed alternative value is
      given.  This will become an error in R 2.13.0.

     StructTS(type = "BSM") now allows series with just two seasons.

(Reported by Birgit Erni.)

  INSTALLATION:      The PDF reference manual is now built as PDF version 1.5 with

      object compression, which on platforms for which this is not the
      default (notably MiKTeX) halves its size.

     Variable FCLIBS can be set during configuration, for any
      additional library flags needed when linking a shared object with
      the Fortran 9x compiler.  (Needed with Solaris Studio 12.2.)

  BUG FIXES:      seq.int() no longer sometimes evaluates arguments twice.

     The data.frame method of format() failed if a column name was       longer than 256 bytes (the maximum length allowed for an R name).

     predict(<lm object>, type ="terms", ...) failed if both terms and       interval were specified. (Reported by Bill Dunlap.)

      Also, if se.fit = TRUE the standard errors were reported for all
      terms, not just those selected by a non-null terms.

     The TRE regular expressions engine could terminate R rather than
      give an error when given certain invalid regular expressions.

cmdscale(eig = TRUE) was documented to return n-1 eigenvalues but in fact only returned k. It now returns all n eigenvalues. cmdscale(add = TRUE) failed to centre the return configuration and sometimes lost the labels on the points. Its return value was described wrongly (it is always a list and contains component ac). promptClass() in package methods now works for reference classes and gives a suitably specialized skeleton of documentation. Also, callSuper() now works via the methods() invocation as well as for initially specified methods. download.file() could leave the destination file open if the URL was not able to be opened. (PR#14414) Assignment of an environment to functions or as an attribute to other objects now works for S4 subclasses of "environment". Use of [[<- for S4 subclasses of "environment" generated an infinite recursion from the method. The method has been replaced by internal code. In a reference class S4 method, callSuper() now works in initialize() methods when there is no explicit superclass method. ! dropped attributes such as names and dimensions from a length-zero argument. (PR#14424) When list2env() created an environment it was missing a PROTECT call and so was vulnerable to garbage collection. Sweave() with keep.source=TRUE dropped comments at the start and end of code chunks. It could also fail when \SweaveInput was combined with named chunks. The Fortran code used by nls(algorithm = "port") could infinite-loop when compiled with high optimization on a modern version of gcc, and SAFE_FFLAGS is now used to make this less likely. (PR#14427, seen with 32-bit Windows using gcc 4.5.0 used from R 2.12.0.) sapply() with default simplify = TRUE and mapply() with default SIMPLIFY = TRUE wrongly simplified language-like results, as, e.g., in mapply(1:2, c(3,7), FUN = function(i,j) call(':',i,j)). Backreferences to undefined patterns in [g]sub(pcre = TRUE) could cause a segfault. (PR#14431) The format() (and hence the print()) method for class "Date" rounded fractional dates towards zero: it now always rounds them down. Reference S4 class creation could generate ambiguous inheritance patterns under very special circumstances. [[<- turned S4 subclasses of "environment" into plain environments. Long titles for help pages were truncated in package indices and a few other places. Additional utilities now work correctly with S4 subclasses of "environment" (rm, locking tools and active bindings). spec.ar() now also work for the "ols" method. (Reported by Hans-Ruedi Kuensch.) The initialization of objects from S4 subclasses of "environment" now allocates a new environment object. R CMD check has more protection against (probably erroneous) example or test output which is invalid in the current locale. qr.X() with column names and pivoting now also pivots the column names. (PR#14438) unit.pmax() and unit.pmin() in package grid gave incorrect results when all inputs were of length 1. (PR#14443) The parser for NAMESPACE files ignored misspelled directives, rather than signalling an error. For 2.12.x a warning will be issued, but this will be correctly reported as an error in later releases. (Reported by Charles Berry.) Fix for subsetting of "raster" objects when only one of i or j is specified. grid.raster() in package grid did not accept "nativeRaster" objects (like rasterImage() does). Rendering raster images in PDF output was resetting the clipping region. Rendering of raster images on Cairo X11 device was wrong, particularly when a small image was being scaled up using interpolation. With Cairo < 1.6, will be better than before, though still a little clunky. With Cairo >= 1.6, should be sweet as. Several bugs fixed in read.DIF(): single column inputs caused errors, cells marked as "character" could be converted to other types, and (in Windows) copying from the clipboard failed.
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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