R Portable Files

CHANGES IN R 3.1.3:

  NEW FEATURES:

    * The internal method of download.file() can now handle files
      larger than 2GB on 32-bit builds which support such files (tested
      on 32-bit R running on 64-bit Windows).

    * kruskal.test() warns on more types of suspicious input.

    * The as.dendrogram() method for "hclust" objects gains a check
      argument protecting against memory explosion for invalid inputs.

    * capabilities() has a new item long.double which indicates if the
      build uses a long double type which is longer than double.

    * nlm() no longer modifies the callback argument in place (a new
      vector is allocated for each invocation, which mimics the
      implicit duplication that occurred in R < 3.1.0); note that this
      is a change from the previously documented behavior. (PR#15958)

    * icuSetCollate() now accepts locale = "ASCII" which uses the basic
      C function strcmp and so collates strings byte-by-byte in
      numerical order.

    * sessionInfo() tries to report the OS version in use (not just
      that compiled under, and including details of Linux
      distributions).

    * model.frame() (used by lm() and many other modelling functions)
      now warns when it drops contrasts from factors.  (Wish of
      PR#16119)

    * install.packages() and friends now accept the value type =
      "binary" as a synonym for the native binary type on the platform
      (if it has one).

    * Single source or binary files can be supplied for
      install.packages(type = "both") and the appropriate type and
      repos = NULL will be inferred.

    * New function pcre_config() to report on some of the configuration
      options of the version of PCRE in use.  In particular, this
      reports if regular expressions using \p{xx} are supported.

    * (Windows.) download.file(cacheOK = FALSE) is now supported when
      internet2.dll is used.

    * browseURL() has been updated to work with Firefox 36.0 which has
      dropped support for the -remote interface.

  INSTALLATION and INCLUDED SOFTWARE:

    * The included version of PCRE has been updated to 8.36.

    * configure accepts MAKEINFO=texi2any as another way to ensure
      texinfo 5.x is used when both 5.x and 4.x are installed.

  UTILITIES:

    * R CMD check now checks the packages used in \donttest sections of
      the examples are specified in the DESCRIPTION file.  (These are
      needed to run the examples interactively.)

    * R CMD check checks for the undeclared use of GNU extensions in
      Makefiles, and for Makefiles with a missing final linefeed.

      R CMD build will correct line endings in all Makefiles, not just
      those in the src directory.

    * R CMD check notes uses of library() and require() in package
      code: see the section 'Suggested packages' of 'Writing R
      Extensions' for good practice.

  DEPRECATED AND DEFUNCT:

    * The configure option --with-valgrind-instrumentation=3 is
      deprecated and will be removed in R 3.2.0.

  BUG FIXES:

    * (Windows.) Rscript.exe was missing a manifest specifying the
      modern style for common controls (e.g., the download progress
      bar).

    * If a package had extra documentation files but no vignette, the
      HTML help system produced an empty index page.

    * The parser now gives an error if a null character is included in
      a string using Unicode escapes. (PR#16046)

    * qr.Q() failed on complex arguments due to pre-3.0(!) typo.
      (PR#16054)

    * abs() failed with named arguments when the argument was complex.
      (PR#16047)

    * "noquote" objects may now be used as columns in dataframes.
      (PR#15997)

    * Some values with extremely long names were printed incorrectly.
      (PR#15999)

    * Extremely large exponents on zero expressed in scientific
      notation (e.g. 0.0e50000) could give NaN.  (PR#15976)

    * download.file() reported downloaded sizes as 0KB if less than
      1MB, only for R 3.1.2 and only on big-endian platforms.

    * prompt() did not escape percent signs in the automatically
      generated usage section of help files.

    * drop.terms() dropped some of the attributes of the object it was
      working with.  (PR#16029)

    * (Windows.) The command completion in Rgui.exe messed up the
      console.  (PR#15791)

    * (Windows.) The choose.files() command returned a blank string
      when the user asked for a single file but cancelled the request.
      (PR#16074)

    * Math2 S4 group generics failed to correctly dispatch "structure"-
      and "nonStructure"-derived classes.

    * loadNamespace() imposed undocumented restrictions on the
      versionCheck parameter.  (Reported by Geoff Lee.)

    * Rare over-runs detected by AddressSanitizer in substr() and its
      replacement version have been avoided.

      _Inter alia_ that fix gives the documented behaviour for
      substr(x, 1, 2) <- "" (subsequently reported as PR#16214).

    * Loading packages incorrectly defining an S4 generic followed by a
      function of the same name caused an erroneous cyclic namespace
      dependency error.

    * Declared vignette encodings are now always passed to the vignette
      engine.

    * Port Tomas Kalibera's fix from R-devel that restores the
      loadMethod() fast path, effectively doubling the speed of S4
      dispatch.

    * power.t.test() and power.prop.test() now make use of the
      extendInt option of uniroot() and hence work in more extreme
      cases.  (PR#15792)

    * If a package was updated and attached when its namespace was
      already loaded, it could end up with parts from one version and
      parts from the other.  (PR#16120)

    * tools:::.Rdconv() didn't accept --encoding= due to a typo.
      (PR#16121)

    * Unix-alike builds without a suitable makeinfo were documented to
      link the missing HTML manuals to CRAN, but did not.

    * save(*, ascii=TRUE) and load() now correctly deal with NaN's.
      (PR#16137)

    * split.Date() retains fractional representations while avoiding
      incomplete class propagation.

    * R_ext/Lapack.h had not been updated for changes made by LAPACK to
      the argument lists of its (largely internal) functions dlaed2 and
      dlaed3.  (PR#16157)

    * RShowDoc("NEWS", "txt") had not been updated for the layout
      changes of R 3.1.0.

    * The xtfrm() method for class "Surv" has been corrected and its
      description expanded.

    * mode(x) <- y would incorrectly evaluate x before changing its
      mode. (PR#16215)

    * besselJ(1, 2^64) and besselY(..) now signal a warning, returning
      NaN instead of typically segfaulting. (Issue 3 of PR#15554)

    * HTML conversion of \href markup in .Rd files did not remove the
      backslash from \% and so gave an invalid URL.  In a related
      change, the \ escape is now required in such URLs.