Update R to 3.1.1

NEW FEATURES:

    * When attach() reports conflicts, it does so compatibly with
      library() by using message().

    * R CMD Sweave no longer cleans any files by default, compatibly
      with versions of R prior to 3.1.0.  There are new options
      --clean, --clean=default and --clean=keepOuts.

    * tools::buildVignette() and tools::buildVignettes() with clean =
      FALSE no longer remove any created files.  buildvignette() gains
      a keep argument for more cleaning customization.

    * The Bioconductor 'version' used by setRepositories() can now be
      set by environment variable R_BIOC_VERSION at runtime, not just
      when R is installed.  (It has been stated that Bioconductor will
      switch from 'version' 2.14 to 'version' 3.0 during the lifetime
      of the R 3.1 series.)

    * Error messages from bugs in embedded Sexpr code in Sweave
      documents now report the source location.

    * type.convert(), read.table() and similar read.*() functions get a
      new numerals argument, specifying how numeric input is converted
      when its conversion to double precision loses accuracy.  The
      default value, "allow.loss" allows accuracy loss, as in R
      versions before 3.1.0.

    * For some compilers, integer addition could overflow without a
      warning.  R's internal code for both integer addition and
      subtraction is more robust now.

    * The function determining the default number of knots for
      smooth.spline() is now exported, as .nknots.smspl().

    * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
      for a = 0, b = 0, or infinite a and b (where they typically
      returned NaN before).

    * Many package authors report that the RStudio graphics device does
      not work correctly with their package's use of dev.new().  The
      new option dev.new(noRStudioGD = TRUE) replaces the RStudio
      override by the default device as selected by R itself, still
      respecting environment variables R_INTERACTIVE_DEVICE and
      R_DEFAULT_DEVICE.

    * readRDS() now returns visibly.

    * Modifying internal logical scalar constants now results in an
      error instead of a warning.

    * install.packages(repos = NULL) now accepts http:// or ftp:// URLs
      of package archives as well as file paths, and will download as
      required.  In most cases repos = NULL can be deduced from the
      extension of the URL.

    * The warning when using partial matching with the $ operator on
      data frames is now only given when
      options("warnPartialMatchDollar") is TRUE.

    * Package help requests like package?foo now try the package foo
      whether loaded or not.

    * General help requests now default to trying all loaded packages,
      not just those on the search path.

    * Added a new function promptImport(), to generate a help page for
      a function that was imported from another package (and presumably
      re-exported, or help would not be needed).


(markd)