R 2.15.0 is released

From: Peter Dalgaard <pd.mes_at_cbs.dk>
Date: Fri, 30 Mar 2012 11:07:41 +0200


The build system rolled up R-2.15.0.tar.gz (codename "Easter Beagle") at 9:00 this morning. This is the first release of the 2.15 series and contains several new features and changes; see the list below for details.

You can get the source code from

  http://cran.r-project.org/src/base/R-2/R-2.15.0.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.

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) = c6cf7cff235e9bd3c823e6a1a3d76cd5
MD5 (INSTALL) = 37adac6d0fbadf25b5a40e3f7535415e
MD5 (NEWS) = 31dee994d35636656c9e254bfb819d7c
MD5 (NEWS.html) = 0551e23b675fa9dc709830d1a4ee738c
MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71
MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db
MD5 (R-latest.tar.gz) = 905f638990492618559202cc1e48a867
MD5 (README) = 296871fcf14f49787910c57b92655c76
MD5 (RESOURCES) = a7a02d98a407c3cb8674d067608f14fc
MD5 (THANKS) = 159efc7bd4ae7b23dda07c1d431657bc
MD5 (R-2/R-2.15.0.tar.gz) = 905f638990492618559202cc1e48a867

This is the relevant part of the NEWS file

CHANGES IN R VERSION 2.15.0:   SIGNIFICANT USER-VISIBLE CHANGES:     o The behaviour of unlink(recursive = TRUE) for a symbolic link to

      a directory has changed: it now removes the link rather than the
      directory contents (just as rm -r does).

      On Windows it no longer follows reparse points (including
      junctions and symbolic links).

  NEW FEATURES:     o Environment variable RD2DVI_INPUTENC has been renamed to       RD2PDF_INPUTENC.     o .Deprecated() becomes a bit more flexible, getting an old       argument.

    o Even data-only packages without R code need a namespace and so       may need to be installed under R 2.14.0 or later.

    o assignInNamespace() has further restrictions on use apart from at

      top-level, as its help page has warned.  Expect it to be disabled
      from programmatic use in the future.

    o system() and system2() when capturing output report a non-zero
      status in the new "status" attribute.

    o kronecker() now has an S4 generic in package methods on which
      packages can set methods.  It will be invoked by X %x% Y if
      either X or Y is an S4 object.

    o pdf() accepts forms like file = "|lpr" in the same way as
      postscript().

    o pdf() accepts file = NULL.  This means that the device does NOT
      create a PDF file (but it can still be queried, e.g., for font
      metric info).

    o format() (and hence print()) on "bibentry" objects now uses
      options("width") to set the output width.

    o legend() gains a text.font argument. (Suggested by Tim Paine,
      PR#14719.)

    o nchar() and nzchar() no longer accept factors (as integer
      vectors).  (Wish of PR#6899.)

    o summary() behaves slightly differently (or more precisely, its
      print() method does).  For numeric inputs, the number of NAs is
      printed as an integer and not a real.  For dates and datetimes,
      the number of NAs is included in the printed output (the latter
      being the wish of PR#14720).

      The "data.frame" method is more consistent with the default
      method: in particular it now applies zapsmall() to
      numeric/complex summaries.

    o The number of items retained with options(warn = 0) can be set by
      options(nwarnings=).

    o There is a new function assignInMyNamespace() which uses the
      namespace of the function it is called from.

    o attach() allows the default name for an attached file to be
      overridden.

    o bxp(), the work horse of boxplot(), now uses a more sensible
      default xlim in the case where at is specified differently from
      1:n, see the discussion on R-devel, <URL:
      https://stat.ethz.ch/pipermail/r-devel/2011-November/062586.html>.

    o New function paste0(), an efficient version of paste(*, sep=""),
      to be used in many places for more concise (and slightly more
      efficient) code.

    o Function setClass() in package methods now returns, invisibly, a
      generator function for the new class, slightly preferred to
      calling new(), as explained on the setClass help page.

    o The "dendrogram" method of str() now takes its default for
      last.str from option str.dendrogram.last.

    o New simple fitted() method for "kmeans" objects.

    o The traceback() function can now be called with an integer       argument, to display a current stack trace. (Wish of PR#14770.)

    o setGeneric() calls can be simplified when creating a new generic

      function by supplying the default method as the def argument.
      See ?setGeneric.

    o serialize() has a new option xdr = FALSE which will use the
      native byte-order for binary serializations.  In scenarios where
      only little-endian machines are involved (these days, close to
      universal) and (un)serialization takes an appreciable amount of
      time this may speed up noticeably transferring data between
      systems.

    o The internal (un)serialization code is faster for long vectors,
      particularly with XDR on some platforms.  (Based on a suggested
      patch by Michael Spiegel.)

    o For consistency, circles with zero radius are omitted by points()
      and grid.circle().  Previously this was device-dependent, but
      they were usually invisible.

    o NROW(x) and NCOL(x) now work whenever dim(x) looks appropriate,
      e.g., also for more generalized matrices.

    o PCRE has been updated to version 8.30.

    o The internal R_Srcref variable is now updated before the browser       stops on entering a function. (Suggestion of PR#14818.)

    o There are 'bare-bones' functions .colSums(), .rowSums(),

      .colMeans() and .rowMeans() for use in programming where ultimate
      speed is required.

    o The formerly internal function .package_dependencies() from
      package tools for calculating (recursive) (reverse) dependencies
      on package databases has been renamed to package_dependencies()
      and is now exported.

    o There is a new function optimHess() to compute the (approximate)
      Hessian for an optim() solution if hessian = TRUE was forgotten.

    o .filled.contour() is a 'bare-bones' function to add a
      filled-contour rectangular plot to an already prepared plot
      region.

    o The stepping in debugging and single-step browsing modes has
      changed slightly: now left braces at the start of the body are
      stepped over for if statements as well as for for and while
      statements.  (Wish of PR#14814.)

    o library() no longer warns about a conflict with a function from
      package:base if the function has the same code as the base one
      but with a different environment.  (An example is Matrix::det().)

    o When deparsing very large language objects, as.character() now
      inserts newlines after each line of approximately 500 bytes,
      rather than truncating to the first line.

    o New function rWishart() generates Wishart-distributed random
      matrices.

    o Packages may now specify actions to be taken when the package is
      loaded (setLoadActions()).

    o options(max.print = Inf) and similar now give an error (instead
      of warnings later).

    o The "difftime" replacement method of units tries harder to
      preserve other attributes of the argument.  (Wish of PR#14839.)

    o poly(raw = TRUE) no longer requires more unique points than the
      degree.  (Requested by John Fox.)

  PACKAGE parallel:

    o There is a new function mcmapply(), a parallel version of       mapply(), and a wrapper mcMap(), a parallel version of Map().

    o A default cluster can be registered by the new function

      setDefaultCluster(): this will be used by default in functions
      such as parLapply().

    o clusterMap() has a new argument .scheduling to allow the use of
      load-balancing.

    o There are new load-balancing functions parLapplyLB() and
      parSapplyLB().

    o makePSOCKCluster() has a new option useXDR = FALSE which can be
      used to avoid byte-shuffling for serialization when all the nodes
      are known to be little-endian (or all big-endian).

  PACKAGE INSTALLATION:     o Non-ASCII vignettes without a declared encoding are no longer       accepted.

    o C/C++ code in packages is now compiled with -NDEBUG to mitigate

      against the C/C++ function assert being called in production use.
      Developers can turn this off during package development with
      PKG_CPPFLAGS = -UNDEBUG.

    o R CMD INSTALL has a new option --dsym which on Mac OS X (Darwin)
      dumps the symbols alongside the .so file: this is helpful when
      debugging with valgrind (and especially when installing packages
      into R.framework).  [This can also be enabled by setting the
      undocumented environment variable PKG_MAKE_DSYM, since R 2.12.0.]

    o R CMD INSTALL will test loading under all installed
      sub-architectures even for packages without compiled code, unless
      the flag --no-multiarch is used.  (Pure R packages can do things
      which are architecture-dependent: in the case which prompted
      this, looking for an icon in a Windows R executable.)

    o There is a new option install.packages(type = "both") which tries
      source packages if binary packages are not available, on those
      platforms where the latter is the default.

    o The meaning of install.packages(dependencies = TRUE) has changed:
      it now means to install the essential dependencies of the named
      packages plus the Suggests, but only the essential dependencies
      of dependencies.  To get the previous behaviour, specify
      dependencies as a character vector.

    o R CMD INSTALL --merge-multiarch is now supported on OS X and
      other Unix-alikes using multiple sub-architectures.

    o R CMD INSTALL --libs-only now by default does a test load on
      Unix-alikes as well as on Windows: suppress with --no-test-load.

  UTILITIES:     o R CMD check now gives a warning rather than a note if it finds

      inefficiently compressed datasets.  With bzip2 and xz compression
      having been available since R 2.10.0, it only exceptionally makes
      sense to not use them.

      The environment variable _R_CHECK_COMPACT_DATA2_ is no longer
      consulted: the check is always done if _R_CHECK_COMPACT_DATA_ has
      a true value (its default).

    o Where multiple sub-architectures are to be tested, R CMD check
      now runs the examples and tests for all the sub-architectures
      even if one fails.

    o R CMD check can optionally report timings on various parts of the
      check: this is controlled by environment variable
      _R_CHECK_TIMINGS_ documented in 'Writing R Extensions'.  Timings

(in the style of R CMD BATCH) are given at the foot of the output
files from running each test and the R code in each vignette. o There are new options for more rigorous testing by R CMD check selected by environment variables - see the 'Writing R Extensions' manual. o R CMD check now warns (rather than notes) on undeclared use of other packages in examples and tests: increasingly people are using the metadata in the DESCRIPTION file to compute information about packages, for example reverse dependencies. o The defaults for some of the options in R CMD check (described in the 'R Internals' manual) have changed: checks for unsafe and .Internal() calls and for partial matching of arguments in R function calls are now done by default. o R CMD check has more comprehensive facilities for checking compiled code and so gives fewer reports on entry points linked into .so/.dll files from libraries (including C++ and Fortran runtimes). Checking compiled code is now done on FreeBSD (as well as the existing supported platforms of Linux, Mac OS X, Solaris and Windows). o R CMD build has more options for --compact-vignettes: see R CMD build --help. o R CMD build has a new option --md5 to add an MD5 file (as done by CRAN): this is used by R CMD INSTALL to check the integrity of the distribution. If this option is not specified, any existing (and probably stale) MD5 file is removed.

  DEPRECATED AND DEFUNCT:     o R CMD Rd2dvi is now defunct: use R CMD Rd2pdf.

    o Options such --max-nsize, --max-vsize and the function

      mem.limits() are now defunct.  (Options --min-nsize and
      --min-vsize remain available.)

    o Use of library.dynam() without specifying all the first three
      arguments is now disallowed.

      Use of an argument chname in library.dynam() including the
      extension .so or .dll (which was never allowed according to the
      help page) is defunct.  This also applies to
      library.dynam.unload() and to useDynLib directives in NAMESPACE
      files.

    o The internal functions .readRDS() and .saveRDS() are now defunct.

    o The off-line help() types "postscript" and "ps" are defunct.

    o Sys.putenv(), replaced and deprecated in R 2.5.0, is finally       removed.

    o Some functions/objects which have been defunct for five or more

      years have been removed completely.  These include .Alias(),
      La.chol(), La.chol2inv(), La.eigen(), Machine(), Platform(),
      Version, codes(), delay(), format.char(), getenv(), httpclient(),
      loadURL(), machine(), parse.dcf(), printNoClass(), provide(),
      read.table.url(), restart(), scan.url(), symbol.C(), symbol.For()
      and unix().

    o The ENCODING argument to .C() is deprecated.  It was intended to
      smooth the transition to multi-byte character strings, but can be
      replaced by the use of iconv() in the rare cases where it is
      still needed.

  INSTALLATION:     o Building with a positive value of --with-valgrind-instrumentation       now also instruments logical, complex and raw vectors.

    o There is experimental support for _link-time optimization_ with       gcc 4.5.0 or later on platforms which support it.

  C-LEVEL FACILITIES:     o Passing R objects other than atomic vectors, functions, lists and

      environments to .C() is now deprecated and will give a warning.
      Most cases (especially NULL) are actually coding errors.  NULL
      will be disallowed in future.

      .C() now passes a pairlist as a SEXP to the compiled code.  This
      is as was documented, but pairlists were in reality handled
      differently as a legacy from the early days of R.

    o call_R and call_S are deprecated.  They still exist in the
      headers and as entry points, but are no longer documented and
      should not be used for new code.

  BUG FIXES:     o str(x, width) now obeys its width argument also for function       headers and other objects x where deparse() is applied.

    o The convention for x %/% 0L for integer-mode x has been changed       from 0L to NA_integer_. (PR#14754)

    o The exportMethods directive in a NAMESPACE file now exports S4

      generics as necessary, as the extensions manual said it does.
      The manual has also been updated to be a little more informative
      on this point.

      It is now required that there is an S4 generic (imported or
      created in the package) when methods are to be exported.

    o Reference methods cannot safely use non-exported entries in the
      namespace.  We now do not do so, and warn in the documentation.

    o The namespace import code was warning when identical S4 generic
      functions were imported more than once, but should not (reported
      by Brian Ripley, then Martin Morgan).

    o merge() is no longer allowed (in some ways) to create a data
      frame with duplicate column names (which confused PR#14786).

    o Fixes for rendering raster images on X11 and Windows devices when
      the x-axis or y-axis scale is reversed.

    o getAnywhere() found S3 methods as seen from the utils namespace
      and not from the environment from which it was called.

    o selectMethod(f, sig) would not return inherited group methods
      when caching was off (as it is by default).

    o dev.copy2pdf(out.type = "cairo") gave an error. (PR#14827)

    o Virtual classes (e.g., class unions) had a NULL prototype even if       that was not a legal subclass. See ?setClassUnion.

    o The C prototypes for zdotc and zdotu in R_ext/BLAS.h have been

      changed to the more modern style rather than that used by f2c.

(Patch by Berwin Turlach.)
o isGeneric() produced an error for primitives that can not have methods. o .C() or .Fortran() had a lack-of-protection error if the registration information resulted in an argument being coerced to another type. o boxplot(x=x, at=at) with non finite elements in x and non integer at could not generate a warning but failed. o heatmap(x, symm=TRUE, RowSideColors=*) no longer draws the colors in reversed order.

    o predict(<ar>) was incorrect in the multivariate case, for p >= 2.

    o print(x, max=m) is now consistent when x is a "Date"; also the

      "reached ... max.print .." messages are now consistently using
      single brackets.

    o Closed the <li> tag in pages generated by Rd2HTML(). (PR#14841.)

    o Axis tick marks could go out of range when a log scale was used.
(PR#14833.)

    o Signature objects in methods were not allocated as S4 objects
(caused a problem with trace() reported by Martin Morgan).

--
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

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