[R] R 3.1.1 is released

[Peter Dalgaard]

The build system rolled up R-3.1.1.tar.gz (codename "Sock it to Me") this morning.

The list below details the changes in this release.

You can get the source code from

http://cran.r-project.org/src/base/R-3/R-3.1.1.tar.gz

or wait for it to be mirrored at a CRAN site nearer to you.

Binaries for various platforms will appear in due course. Perhaps with some delays due to vacations. In particular, the Mac OS X maintainer is traveling and may be without Internet access for some days yet.

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) = cbf6da8f886ccd8d0dda0cc7ffd1b8ec
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 19b98552686c3f3c95a6028596c533e9
MD5 (INSTALL) = 3964b9119adeaab9ceb633773fc94aac
MD5 (NEWS) = bf2c79e7fd7e2dff621a3a8410c89bb4
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = e840d32b7ef7a7603455d30d6d54fda7
MD5 (NEWS.html) = 206dc0c4dc31004f245813b403ec6d6a
MD5 (R-latest.tar.gz) = 2598f5bbbedb00e463e0c1385e6fe999
MD5 (README) = aece1dfbd18c1760128c3787f5456af6
MD5 (RESOURCES) = c7cb32499ebbf85deb064aab282f93a4
MD5 (THANKS) = d4b45e302b7cad0fc4bb50d2cfe69649
MD5 (R-3/R-3.1.1.tar.gz) = 2598f5bbbedb00e463e0c1385e6fe999


This is the relevant part of the NEWS file


  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.  (PR#15774)

    * 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).

  INSTALLATION and INCLUDED SOFTWARE:

    * configure option --with-internal-tzcode can now be used with
      variable rsharedir.

    * The included version of PCRE has been updated to 8.35.

    * There is a new target make uninstall-libR to remove an installed
      shared/static libR.

      make install-libR now works if a sub-architecture is used,
      although the user will need to specify libdir differently for
      different sub-architectures.

    * There is more extensive advice on which LaTeX packages are
      required to install R or to make package manuals (as done by R
      CMD check) in the 'Writing R Extensions' manual.

    * Compilers/linkers were handling the visibility controls in
      src/extra/xz inconsistently (and apparently in some cases
      incorrectly), so it has been simplified.  (PR#15327)

    * (Windows) There is updated support for the use of ICU for
      collation: see the 'R Installation and Administration Manual'.

  BUG FIXES:

    * dbinom(x, n), pbinom(), dpois(), etc, are slightly less
      restrictive in checking if n is integer-valued.  (Wish of
      PR#15734.)

    * pchisq(x, df, ncp, log.p = TRUE) is more accurate and no longer
      underflows for small x and ncp < 80, e.g, for pchisq(1e-5, df =
      100, ncp = 1, log = TRUE).  (Based on PR#15635 and a suggestion
      by Roby Joehanes.)

    * The s ("step into") command in the debugger would cause R to step
      into expressions evaluated there, not just into functions being
      debugged.  (PR#15770)

    * The C code used by strptime() rejected time-zone offsets of more
      than +1200 (+1245, +1300 and +1400 can occur).  (PR#15768)

    * (Windows only.)  png(type = "cairo", antialias = "gray") was not
      accepted.  (PR#15760)

    * Use of save(..., envir=) with named objects could fail.
      (PR#15758)

    * Sweave() mis-parsed Sexpr expressions that contained backslashes.
      (PR#15779)

    * The return value from options(foo = NULL) was not the previous
      value of the option.  (PR#15781)

    * enc2utf8() and enc2native() did not always mark the encoding of
      the return values when it was known.

    * dnbinom(x, size = <large>, mu, log = TRUE) no longer underflows
      to -Inf for large mu, thanks to a suggestion from Alessandro
      Mammana (MPI MolGen, Berlin).

    * pbeta(x, a, b, log = TRUE) no longer behaves discontinuously (in
      a small x-region) because of denormalized numbers.  Also,
      pbeta(1-1e-12, 1e30, 1.001, log=TRUE) now terminates "in real
      time".

    * The "CRAN" filter (see available.packages()) no longer removes
      duplicates other than of packages on CRAN, and does not fail if
      there is no CRAN repository in getOption("repos").

    * The device listing from dev2bitmap() and bitmap() was truncated
      to 1000 characters: modern versions of GhostScript on most
      platforms have many more devices.

    * (Windows.)  Commands such as Sys.which() and pipe() which needed
      to find the full path to a command could segfault if the 'long'
      path name was much longer than the 'short' path name (which
      Sys.which() returns), as the behaviour of the Windows API call
      had changed.

    * R CMD build will fail with an error if one of the packages
      specified in the VignetteBuilder field is not installed.
      (Without loading those packages it cannot be ascertained which
      files are intended to be vignettes. This means that the
      VignetteBuilder packages have to be installed for package
      checking too.)  (Wish of PR#15775.)

    * Misguided attempts to use chull() with non-finite points now give
      an error (related to PR#15777).

    * For a formula with exactly 32 variables the 32nd variable was
      aliased to the intercept in some C-level computations of terms,
      so that for example attempting to remove it would remove the
      intercept instead (and leave a corrupt internal structure).
      (PR#15735)

    * anyDuplicated() silently returned wrong values when the first
      duplicate was at an index which was too large to be stored in an
      integer vector (although a lot of RAM and patience would have
      been needed to encounter this).

    * tools::Rd2ex(commentDontrun = FALSE) failed if the block had only
      one line.

    * Hexadecimal constants such as 0x110p-5L which were incorrectly
      qualified by L were parsed incorrectly since R 3.0.0, with a
      slightly garbled warning. (PR#15753)

    * system() returned success on some platforms even if the system
      was unable to launch a process. (PR#15796)

    * (Windows Rgui console.)  Unbuffered output was sometimes not
      output immediately if the prompt was not on the last line of the
      console.

    * The built-in help server did not declare the encoding for the
      DESCRIPTION or other text files to be the package encoding, so
      non-ASCII characters could be displayed incorrectly.

    * R is now trying harder to not cleanup child processes that were
      not spawned by mcparallel() on platforms that provide information
      about the source process of the SIGCHLD signal. This allows 3rd
      party libraries to manage the exit status of children that they
      spawn without R interfering.

    * mcmapply() was only parallelizing if the number of jobs was
      bigger than the number of cores. It now parallelizes if the
      number of jobs is more than one.

    * Auto-printing would re-evaluate its argument when trying to
      dispatch to a print method.  This is now avoided when possible.

    * Unserializing (including load() and readRDS()) could silently
      return incorrect numeric values from ASCII saves if there was a
      read error.

    * getParseData() could return incorrect values for the parents of
      some elements. (Reported by Andrew Redd.)

    * Attempting to use data frames of 2^31 or more rows with merge()
      or to create a merged data frame of that size now gives a clearer
      error message.

    * parse() did not check its file argument was a connection if it
      was not a character string, so e.g. parse(FALSE) attempted to
      read from stdin.

      Nor did dump() and dput().

    * The "help.try.all.packages" option was ignored when the shortcut
      syntax for help was used, e.g. ?foo.

    * A potential segfault in string allocation has been fixed.  (Found
      by Radford Neal.)

    * Potential memory protection errors in sort() and D() have been
      fixed. (Found by Radford Neal.)

    * Fixed a lack of error checking in graphics event functions.
      (Found by Radford Neal; a different patch used here than the one
      in pqR.)

    * numericDeriv() sometimes miscalculated the gradient.  (PR#15849,
      reported originally by Radford Neal)



-- 
Peter Dalgaard, Professor,
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