R Portable Files

CHANGES IN R 3.1.2:

  NEW FEATURES:

    * embedFonts() now defaults to format = "ps2write" for .ps and .eps
      files.  This is available in Ghostscript 9.x (since 2010) whereas
      the previous default, format = "pswrite", was removed in
      Ghostscript 9.10.

    * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
      point mass at exp(mulog) rather than return NaN (for an error).

    * capabilities() now reports if ICU is compiled in for use for
      collation (it is only actually used if a suitable locale is set
      for collation, and never for a C locale).

    * (OS X only.) Package tcltk checks when loaded if it is linked
      against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
      component and the X11 libraries are installed.  This allows more
      informative error messages to be given advising the installation
      of the missing component or of XQuartz.

      The X11() device and X11-based versions of the data editor and
      viewer (invoked by edit() and View() for data frames and matrices
      from command-line R) check that the X11 libraries are installed
      and if not advises installing XQuartz.

    * icuSetCollate() allows locale = "default", and locale = "none" to
      use OS services rather than ICU for collation.

      Environment variable R_ICU_LOCALE can be used to set the default
      ICU locale, in case the one derived from the OS locale is
      inappropriate (this is currently necessary on Windows).

    * New function icuGetCollate() to report on the ICU collation
      locale in use (if any).

    * utils::URLencode() was updated to use unreserved and reserved
      characters from RFC 3986, <URL:
      http://tools.ietf.org/html/rfc3986>, instead of RFC 1738.

    * unique(warnings()) and c(warnings()) are now supported.

    * The Bioconductor 'version' used by setRepositories() now defaults
      to 3.0. (It can be set at runtime _via_ environment variable
      R_BIOC_VERSION.)

  INSTALLATION and INCLUDED SOFTWARE:

    * The configure script reports on the more important
      capabilities/options which will not be compiled in.

      More types of external BLAS are recognized by name in that
      report.

    * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
      flag is placed earlier in the link commands used during
      installation and when packages are installed: this helps ensure
      that the current build has priority if an R shared library has
      already been installed by e.g. install-libR in a library
      mentioned in LDFLAGS (and not in 'your system's library
      directory' as documented). (Wish of PR#15790.)

    * LaTeX package upquote is no longer required for R's use of
      inconsolata.

    * (Windows only) If both 32 and 64 bit versions of R are installed,
      the bin/R.exe and bin/Rscript.exe executables now run 64 bit R.
      (To run 32 bit R, overwrite these files with copies of
      bin/i386/Rfe.exe.)

  UTILITIES:

    * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
      the VignetteBuilder packages available even if they are listed in
      Suggests, since they are needed to recognise and process
      non-Sweave vignettes.

    * R CMD check now reports empty importFrom declarations in a
      NAMESPACE file, as these are common errors (writing
      importFrom(Pkg) where import(Pkg) was intended).

    * R CMD check now by default checks code usage directly on the
      package namespace without loading and attaching the package and
      its suggests and enhances.  For good practice with packages in
      the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'.  For
      use of lazy-data objects in the package's own code, see ?data.

  BUG FIXES:

    * dmultinom() did not handle non-finite probabilities correctly.

    * prettyNum(x, zero.print=*) now also works when x contains NAs.

    * A longstanding bug exhibited by nlminb() on Windows was traced to
      a compiler bug in gcc 4.6.3; a workaround has been put in place.
      (PR#15244 and PR#15914).

    * Rendering of \command in HTML versions of help pages has been
      improved: this is particularly evident on the help page for
      INSTALL.

    * as.hexmode(x) and as.octmode(x) now behave correctly for some
      numeric x, e.g., c(NA, 1) or c(1, pi).

    * drop1() failed if the scope argument had no variables to drop.
      (PR#15935)

    * edit() (and hence fix()) failed if an object had a non-character
      attribute named "source" (an attribute that had been used in R
      prior to version 2.14.0).

    * callGeneric() could fail if the generic had ... as a formal
      argument. (PR#15937).

    * Forking in package parallel called C entry point exit in the
      child.  This was unsafe (_exit should have been called), and
      could flush stdin of the main R process (seen most often on
      Solaris).

      As good practice, stdout is now flushed before forking a child.

    * R objects such as list(`a\b` = 1) now print correctly.

    * getAnywhere("C_pbinom") now returns correctly a single object
      (rather than unlisting it).

    * The confint() method for nls() fits failed it these has specified
      parameter limits despite using an algorithm other than "port".
      (PR#15960)

    * Subclassing an S4 class failed if the class required arguments to
      the generator, through its initialize() method.

    * removeSource() did not properly handle expressions containing
      arguments that were supplied as missing, e.g.  x[i,]. (PR#15957)

    * as.environment(list()) now works, and as.list() of such an
      environment is now the same as list().

    * Several tcltk functions failed when run in unusual environments.
      (PR#15970)

    * options(list()) now works (trivially). (PR#15979)

    * merge(<dendrogram>, ..) now works correctly for two `independent'
      dendrograms (PR#15648), and still compatibly via adjust = "auto"
      e.g. for two branches of an existing dendrogram.

    * The plot method for "hclust" objects gets an optional argument
      check; When that is true (the default) it checks more carefully
      for valid input.

    * (Windows only) If a user chose to install 64 bit R but not 32 bit
      R, the bin/R and bin/Rscript executables failed to run.
      (PR#15981)

    * Various possible buffer overruns have been prevented, and missed
      memory protection added. (PR#15990)

    * Rscript no longer passes --args to R when there are no extra
      ("user") arguments.

    * objects like getClass("refClass")@prototype now print() and str()
      without error.

    * identical() now also looks at the S4 bit.

    * hist(x, breaks) is more robust in adding a small fuzz to few
      breaks when some are very large. (PR#15988)

    * sub() and gsub() did not handle regular expressions like "\s{2,}"
      properly if the text contained NA or non-ascii elements in a
      UTF-8 locale.  Part of this was due to a bug in the TRE library.
      (PR#16009)

    * RShowDoc("NEWS") now displays the PDF version.

    * Matrices and arrays with last dimension zero did not print at all
      or incompletely.  (PR#16012)

    * plot.histogram() and hence hist() now respect the xaxs, yaxs and
      lab graphics parameters.  (PR#16021)

    * bw.SJ(x) and other bw.*() no longer segfault when x contains
      non-finite values. (PR#16024)

    * R CMD Rd2pdf unintentionally ignored its --os option.

    * The internal method of download.file() was not reporting file
      sizes and progress correctly on files larger than 2GB (inherited
      from libxml2).  This is corrected for 64-bit builds (32-bit
      platforms may not support such files, but where possible will be
      supported in future versions of R).

    * Work around a bug in OS X Yosemite where key environment
      variables may be duplicated causing issues in subprocesses. The
      duplicates are now removed on R startup (via Rprofile).
      (PR#16042)

    * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
      latest XQuartz.