R News

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.



  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.



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).



  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

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.

CHANGES IN R 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.



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.



Compilers/linkers were handling the visibility control 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

  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 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

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.



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)

CHANGES IN R 3.1.0:

  NEW FEATURES:

type.convert() (and hence by default read.table()) returns a character
      vector or factor when representing a numeric input as a double
      would lose accuracy.  Similarly for complex inputs.

      If a file contains numeric data with unrepresentable numbers of
      decimal places that are intended to be read as numeric, specify
      colClasses in read.table() to be "numeric".

tools::Rdiff(useDiff = FALSE) is closer to the POSIX definition of diff
      -b (as distinct from the description in the man pages of most
      systems).

New function anyNA(), a version of any(is.na(.)) which is fast for
      atomic vectors, based on a proposal by Tim Hesterberg. (Wish of
      PR#15239.)

arrayInd(*, useNames = TRUE) and, analogously, which(*, arr.ind = TRUE)
      now make use of names(.dimnames) when available.

is.unsorted() now also works for raw vectors.

The "table" method for as.data.frame() (also useful as
      as.data.frame.table()) now passes sep and base arguments to
      provideDimnames().

uniroot() gets new optional arguments, notably extendInt, allowing to
      auto-extend the search interval when needed.  The return value
      has an extra component, init.it.

switch(f, ...) now warns when f is a factor, as this typically happens
      accidentally where the useR meant to pass a character string, but
      f is treated as integer (as always documented).

The parser has been modified to use less memory.

The way the unary operators (+ - !) handle attributes is now more
      consistent.  If there is no coercion, all attributes (including
      class) are copied from the input to the result: otherwise only
      names, dims and dimnames are.

colorRamp() and colorRampPalette() now allow non-opaque colours and a
      ramp in opacity via the new argument alpha = TRUE.  (Suggested by
      Alberto Krone-Martins, but optionally as there are existing uses
      which expect only RGB values.)

grid.show.layout() and grid.show.viewport() get an optional vp.ex
      argument.

There is a new function find_gs_cmd() in the tools package to locate a
      GhostScript executable.  (This is an enhanced version of a
      previously internal function there.)

object.size() gains a format() method.

There is a new family, "ArialMT", for the pdf() and postscript()
      devices.  This will only be rendered correctly on viewers which
      have access to Monotype TrueType fonts (which are sometimes
      requested by journals).

The text and PDF news files, including NEWS and NEWS.2, have been moved
      to the doc directory.

combn(x, simplify = TRUE) now gives a factor result for factor input x
      (previously user error).  (Related to PR#15442.)

Added utils::fileSnapshot() and utils::changedFiles() functions to
      allow snapshots and comparison of directories of files.

make.names(names, unique=TRUE) now tries to preserve existing names.
      (Suggestion of PR#15452.)

New functions cospi(x), sinpi(x), and tanpi(x), for more accurate
      computation of cos(pi*x), etc, both in R and the C API.  Using
      these gains accuracy in some cases, e.g., inside lgamma() or
      besselI().  (Suggested by Morten Welinder in PR#15529.)

print.table(x, zero.print = ".") now also has an effect when x is not
      integer-valued.

There is more support to explore the system's idea of time-zone names.
      Sys.timezone() tries to give the current system setting by name
      (and succeeds at least on Linux, OS X, Solaris and Windows), and
      OlsonNames() lists the names in the system's Olson database.
      Sys.timezone(location = FALSE) gives the previous behaviour.

Platforms with a 64-bit time_t type are allowed to handle conversions
      between the "POSIXct" and "POSIXlt" classes for date-times
      outside the 32-bit range (before 1902 or after 2037): the
      existing workarounds are used on other platforms.  (Note that
      time-zone information for post-2037 is speculative at best, and
      the OS services are tested for known errors and so not used on OS
      X.)

      Currently time_t is usually long and hence 64-bit on Unix-alike
      64-bit platforms: however in several cases the time-zone database
      is 32-bit.  For R for Windows it is 64-bit (for both
      architectures as from this version).

The "save.defaults" option can include a value for compression_level.
      (Wish of PR#15579.)

colSums() and friends now have support for arrays and data-frame
      columns with 2^31 or more elements.

as.factor() is faster when f is an unclassed integer vector (for
      example, when called from tapply()).

fft() now works with longer inputs, from the 12 million previously
      supported up to 2 billion.  (PR#15593)

Complex svd() now uses LAPACK subroutine ZGESDD, the complex analogue
      of the routine used for the real case.

Sweave now outputs .tex files in UTF-8 if the input encoding is
      declared to be UTF-8, regardless of the local encoding.  The
      UTF-8 encoding may now be declared using a LaTeX comment
      containing the string %\SweaveUTF8 on a line by itself.

file.copy() gains a copy.date argument.

Printing of date-times will make use of the time-zone abbreviation in
      use at the time, if known.  For example, for Paris pre-1940 this
      could be LMT, PMT, WET or WEST.  To enable this, the "POSIXlt"
      class has an optional component "zone" recording the abbreviation
      for each element.

      For platforms which support it, there is also a component
      "gmtoff" recording the offset from GMT where known.

(On Windows, by default on OS X and optionally elsewhere.)  The system
      C function strftime has been replaced by a more comprehensive
      version with closer conformance to the POSIX 2008 standard.

dnorm(x, log = FALSE) is more accurate (but somewhat slower) for |x| >
      5; as suggested in PR#15620.

Some versions of the tiff() device have further compression options.

read.table(), readLines() and scan() have a new argument to influence
      the treatment of embedded nuls.

Avoid duplicating the right hand side values in complex assignments
      when possible.  This reduces copying of replacement values in
      expressions such as Z$a <- a0 and ans[[i]] <- tmp: some package
      code has relied on there being copies.

      Also, a number of other changes to reduce copying of objects; all
      contributed by or based on suggestions by Michael Lawrence.

The fast argument of KalmanLike(), KalmanRun() and KalmanForecast() has
      been replaced by update, which instead of updating mod in place,
      optionally returns the updated model in an attribute "mod" of the
      return value.

arima() and makeARIMA() get a new optional argument SSinit, allowing
      the choice of a different *s*tate *s*pace initialization which
      has been observed to be more reliable close to non-stationarity:
      see PR#14682.

warning() has a new argument noBreaks., to simplify post-processing of
      output with options(warn = 1).

pushBack() gains an argument encoding, to support reading of UTF-8
      characters using scan(), read.table() and related functions in a
      non-UTF-8 locale.

all.equal.list() gets a new argument use.names which by default labels
      differing components by names (if they match) rather than by
      integer index.  Saved R output in packages may need to be
      updated.

The methods for all.equal() and attr.all.equal() now have argument
      check.attributes after ... so it cannot be partially nor
      positionally matched (as it has been, unintentionally).

      A side effect is that some previously undetected errors of
      passing empty arguments (no object between commas) to all.equal()
      are detected and reported.

      There are explicit checks that check.attributes is logical,
      tolerance is numeric and scale is NULL or numeric.  This catches
      some unintended positional matching.

      The message for all.equal.numeric() reports a "scaled difference"
      only for scale != 1.

all.equal() now has a "POSIXt" method replacing the "POSIXct" method.

The "Date" and "POSIXt" methods of seq() allows by = "quarter" for
      completeness (by = "3 months" always worked).

file.path() removes any trailing separator on Windows, where they are
      invalid (although sometimes accepted).  This is intended to
      enhance the portability of code written by those using POSIX file
      systems (where a trailing / can be used to confine path matching
      to directories).

New function agrepl() which like grepl() returns a logical vector.

fifo() is now supported on Windows. (PR#15600)

sort.list(method = "radix") now allows negative integers (wish of
      PR#15644).

Some functionality of print.ts() is now available in .preformat.ts()
      for more modularity.

mcparallel() gains an option detach = TRUE which allows execution of
      code independently of the current session.  It is based on a new
      estranged = TRUE argument to mcfork() which forks child processes
      such that they become independent of the parent process.

The pdf() device omits circles and text at extremely small sizes, since
      some viewers were failing on such files.

The rightmost break for the "months", "quarters" and "years" cases of
      hist.POSIXlt() has been increased by a day.  (Inter alia, fixes
      PR#15717.)

The handling of DF[i,] <- a where i is of length 0 is improved.  (Inter
      alia, fixes PR#15718.)

hclust() gains a new method "ward.D2" which implements Ward's method
      correctly.  The previous "ward" method is "ward.D" now, with the
      old name still working.  Thanks to research and proposals by
      Pierre Legendre.

The sunspot.month dataset has been amended and updated from the
      official source, whereas the sunspots and sunspot.year datasets
      will remain immutable. The documentation and source links have
      been updated correspondingly.

The summary() method for "lm" fits warns if the fit is essentially
      perfect, as most of the summary may be computed inaccurately (and
      with platform-dependent values).

      Programmers who use summary() in order to extract just a
      component which will be reliable (e.g., $cov.unscaled) should
      wrap their calls in suppressWarnings().

  INSTALLATION and INCLUDED SOFTWARE:

The included version of LAPACK has been updated to 3.5.0.

There is some support for parallel testing of an installation, by
      setting TEST_MC_CORES to an integer greater than one to indicate
      the maximum number of cores to be used in parallel. (It is worth
      specifying at least 8 cores if available.)  Most of these require
      a make program (such as GNU make and dmake) which supports the
      $MAKE -j nproc syntax.

      Except on Windows: the tests of standard package examples in make
      check are done in parallel.  This also applies to running
      tools::testInstalledPackages().

      The more time-consuming regression tests are done in parallel.

      The package checks in make check-devel and make check-recommended
      are done in parallel.

More of make check will work if recommended packages are not installed:
      but recommended packages remain needed for thorough checking of
      an R build.

The version of tzcode included in src/extra/tzone has been updated.
      (Formerly used only on Windows.)

The included (64-bit) time-zone conversion code and Olson time-zone
      database can be used instead of the system version: use configure
      option --with-internal-tzcode.  This is the default on Windows
      and OS X.  (Note that this does not currently work if a
      non-default rsharedir configure variable is used.)

      (It might be necessary to set environment variable TZ on OSes
      where this is not already set, although the system timezone is
      deduced correctly on at least Linux, OS X and Windows.)

      This option also switches to the version of strftime included in
      directory src/extra/tzone.

configure now tests for a C++11-compliant compiler by testing some
      basic features.  This by default tries flags for the compiler
      specified by CXX, but an alternative compiler, options and
      standard can be specified by variables CXX1X, CXX1XFLAGS and
      CXX1XSTD (e.g., -std=gnu++11).

R can now optionally be compiled to use reference counting instead of
      the NAMED mechanism by defining SWITCH_TO_REFCNT in Rinternals.h.
      This may become the default in the future.

There is a new option --use-system-tre to use a suitable system tre
      library: at present this means a version from their git
      repository, after corrections.  (Wish of PR#15660.)

  PACKAGE INSTALLATION:

The CRANextra repository is no longer a default repository on Windows:
      all the binary versions of packages from CRAN are now on CRAN,
      although CRANextra contains packages from Omegahat and elsewhere
      used by CRAN packages.

Only vignettes sources in directory vignettes are considered to be
      vignettes and hence indexed as such.

In the DESCRIPTION file,
      
          License: X11

      is no longer recognized as valid.  Use MIT or BSD_2_clause
      instead, both of which need + file LICENSE.

For consistency, entries in .Rinstignore are now matched
      case-insensitively on all platforms.

Help for S4 methods with very long signatures now tries harder to split
      the description in the Usage field to no more than 80 characters
      per line (some packages had over 120 characters).

R CMD INSTALL --build (not Windows) now defaults to the internal tar()
      unless R_INSTALL_TAR is set.

There is support for compiling C++11 code in packages on

Fake installs now install the contents of directory inst: some packages
      use this to install e.g. C++ headers for use by other packages
      that are independent of the package itself.  Option --no-inst can
      be used to get the previous behaviour.

  DEBUGGING:

The behaviour of the code browser has been made more consistent, in
      part following the suggestions in PR#14985.

Calls to browser() are now consistent with calls to the browser
      triggered by debug(), in that Enter will default to n rather than
      c.

A new browser command s has been added, to

A new browser command f has been added, to

Within the browser, the command help will display a short list of
      available commands.

  UTILITIES:

Only vignettes sources in directory vignettes are considered to be
      vignettes by R CMD check.  That has been the preferred location
      since R 2.14.0 and is now obligatory.

For consistency, R CMD build now matches entries in .Rbuildignore and
      vignettes/.install_extras case-insensitively on all platforms
      (not just on Windows).

checkFF() (called by R CMD check by default) can optionally check
      foreign function calls for consistency with the registered type
      and argument count.  This is the default for R CMD check
      --as-cran or can be enabled by setting environment variable
      _R_CHECK_FF_CALLS_ to registration (but is in any case suppressed
      by --install=no).  Because this checks calls in which .NAME is an
      R object and not just a literal character string, some other
      problems are detected for such calls.

      Functions suppressForeignCheck() and dontCheck() have been added
      to allow package authors to suppress false positive reports.

R CMD check --as-cran warns about a false value of the DESCRIPTION
      field BuildVignettes for Open Source packages, and ignores it.
      (An Open Source package needs to have complete sources for its
      vignettes which should be usable on a suitably well-equipped
      system).

R CMD check --no-rebuild-vignettes is defunct:
      R CMD check --no-build-vignettes has been preferred since R
      3.0.0.

R CMD build --no-vignettes is defunct:
      R CMD build --no-build-vignettes has been preferred since R
      3.0.0.

R CMD Sweave and R CMD Stangle now process both Sweave and non-Sweave
      vignettes.  The tools::buildVignette() function has been added to
      do the same tasks from within R.

The flags returned by R CMD config --ldflags and (where installed)
      pkg-config --libs libR are now those needed to link a front-end
      against the (shared or static) R library.

Sweave.sty has a new option [inconsolata].

R CMD check customizations such as _R_CHECK_DEPENDS_ONLY_ make
      available packages only in LinkingTo only for installation, and
      not for loading/runtime tests.

tools::checkFF() reports on .C and .Fortran calls with DUP = FALSE if
      argument check_DUP is true.  This is selected by R CMD check by
      default.

R CMD check --use-gct can be tuned to garbage-collect less frequently
      using gctorture2() _via_ the setting of environment variable
      _R_CHECK_GCT_N_.

Where supported, tools::texi2dvi() limits the number of passes tried to
      20.

  C-LEVEL FACILITIES:

(Windows only) A function R_WaitEvent() has been added (with
      declaration in headerR.h) to block execution until the next event
      is received by R.

Remapping in the Rmath.h header can be suppressed by defining
      R_NO_REMAP_RMATH.

The remapping of rround() in header Rmath.h has been removed: use
      fround() instead.

ftrunc() in header Rmath.h is now a wrapper for the C99 function
      trunc(), which might as well be used in C code: ftrunc() is still
      needed for portable C++ code.

The never-documented remapping of prec() to fprec() in header Rmath.h
      has been removed.

The included LAPACK subset now contains ZGESDD and ZGELSD.

The function LENGTH() now checks that it is only applied to vector
      arguments.  However, in packages length() should be used. (In R
      itself LENGTH() is a macro without the function overhead of
      length().)

Calls to SET_VECTOR_ELT() and SET_STRING_ELT() are now checked for
      indices which are in-range: several packages were writing one
      element beyond the allocated length.

allocVector3 has been added which allows custom allocators to be used
      for individual vector allocations.

  DEPRECATED AND DEFUNCT:

chol(pivot = TRUE, LINPACK = TRUE) is defunct.

      Arguments EISPACK for eigen() and LINPACK for chol(), chol2inv(),
      solve() and svd() are ignored: LAPACK is always used.

.find.package() and .path.package() are defunct: only the versions
      without the initial dot introduced in R 2.13.0 have ever been in
      the API.

Partial matching when using the $ operator _on data frames_ now throws
      a warning and may become defunct in the future. If partial
      matching is intended, replace foo$bar by foo[["bar", exact =
      FALSE]].

The long-deprecated use of \synopsis in the Usage section of .Rd files
      has been removed: such sections are now ignored (with a warning).

package.skeleton()'s deprecated argument namespace has been removed.

Many methods are no longer exported by package stats.  They are all
      registered on their generic, which should be called rather than
      calling a method directly.

Functions readNEWS() and checkNEWS() in package tools are defunct.

download.file(method = "lynx") is deprecated.

.C(DUP = FALSE) and .Fortran(DUP = FALSE) are now deprecated, and may
      be disabled in future versions of R.  As their help has long
      said, .Call() is much preferred.

      R CMD check notes such usages (by default).

The workaround of setting R_OSX_VALGRIND has been removed: it is not
      needed in current valgrind.

  BUG FIXES:

Calling lm.wfit() with no non-zero weights gave an array-overrun in the
      Fortran code and a not very sensible answer.  It is now
      special-cased with a simpler answer (no qr component).

Error messages involving non-syntactic names (e.g., as produced by `\r`
      when that object does not exist) now encode the control
      characters.  (Reported by Hadley Wickham.)

getGraphicsEvent() caused 100% usage of one CPU in Windows. (PR#15500)

nls() with no start argument may now work inside another function
      (scoping issue).

pbeta() and similar work better for very large (billions) ncp.

Where time zones have changed abbreviations over the years, the
      software tries to more consistently use the abbreviation
      appropriate to the time or if that is unknown, the current
      abbreviation.  On some platforms where the C function localtime
      changed the tzname variables the reported abbreviation could have
      been that of the last time converted.

all.equal(list(1), identity) now works.

Bug fix for pushing viewports in grid (reported by JJ Allaire and Kevin
      Ushey).

      NOTE for anyone poking around within the graphics engine display
      list (despite the warnings not to) that this changes what is
      recorded by grid on the graphics engine display list.

Extra checks have been added for unit resolution and conversion in
      grid, to catch instances of division-by-zero.  This may introduce
      error messages in existing code and/or produce a different result
      in existing code (but only where a non-finite location or
      dimension may now become zero).

Some bugs in TRE have been corrected by updating from the git
      repository.  This allows R to be installed on some platforms for
      which this was a blocker (PR#15087 suggests Linux on ARM and
      HP-UX).

? applied to a call to an S4 generic failed in several cases.
      (PR#15680)

The implicit S4 generics for primitives with ... in their argument list
      were incorrect. (PR#15690)

Bug fixes to methods::callGeneric(). (PR#15691)

The bug fix to aggregrate() in PR#15004 introduced a new bug in the
      case of no grouping variables. (PR#15699)

In rare cases printing deeply nested lists overran a buffer by one byte
      and on a few platforms segfaulted. (PR#15679)

The dendrogram method of as.dendrogram() was hidden accidentally,
      (PR#15703), and order.dendrogram(d) gave too much for a leaf d.
      (PR#15702)

R would try to kill processes on exit that have pids ever used by a
      child process spawned by mcparallel even though the current
      process with that pid was not actually its child.

cophenetic() applied to a "dendrogram" object sometimes incorrectly
      returned a "Labels" attribute with dimensions.  (PR#15706)

printCoefmat() called from quite a few print() methods now obeys small
      getOption("width") settings, line wrapping the "signif. codes"
      legend appropriately.  (PR#15708)

model.matrix() assumed that the stored dimnames for a matrix was NULL
      or length 2, but length 1 occurred.

The clipping region for a device was sometimes used in base graphics
      before it was set.

CHANGES IN R 3.0.3:

  NEW FEATURES:

On Windows there is support for making .texi manuals using texinfo 5.0
      or later: the setting is in file src/gnuwin32/MkRules.dist.

      A packaging of the Perl script and modules for texinfo 5.2 has
      been made available at <URL:
      http://www.stats.ox.ac.uk/pub/Rtools/>.

write.table() now handles matrices of 2^31 or more elements, for those
      with large amounts of patience and disc space.

There is a new function, La_version(), to report the version of LAPACK
      in use.



There is some support to produce manuals in ebook formats. (See
      doc/manual/Makefile.  Suggested by Mauro Cavalcanti.)

On a Unix-alike Sys.timezone() returns NA if the environment variable
      TZ is unset, to distinguish it from an empty string which on some
      OSes means the UTC time zone.

The backtick may now be escaped in strings, to allow names containing
      them to be constructed, e.g. `\``.  (PR#15621)

read.table(), readLines() and scan() now warn when an embedded nul is
      found in the input.  (Related to PR#15625 which was puzzled by
      the behaviour in this unsupported case.)

(Windows only.)  file.symlink() works around the undocumented
      restriction of the Windows system call to backslashes.  (Wish of
      PR#15631.)

KalmanForecast(fast = FALSE) is now the default, and the help contains
      an example of how fast = TRUE can be used in this version.  (The
      usage will change in 3.1.0.)

strptime() now checks the locale only when locale-specific formats are
      used and caches the locale in use: this can halve the time taken
      on OSes with slow system functions (e.g., OS X).

strptime() and the format() methods for classes "POSIXct", "POSIXlt"
      and "Date" recognize strings with marked encodings: this allows,
      for example, UTF-8 French month names to be read on (French)
      Windows.

iconv(to = "utf8") is now accepted on all platforms (some
      implementations did already, but GNU libiconv did not: however
      converted strings were not marked as being in UTF-8).  The
      official name, "UTF-8" is still preferred.

available.packages() is better protected against corrupt metadata
      files.  (A recurring problem with Debian package shogun-r:
      PR#14713.)

Finalizers are marked to be run at garbage collection, but run only at
      a somewhat safer later time (when interrupts are checked).  This
      circumvents some problems with finalizers running arbitrary code
      during garbage collection (the known instances being running
      options() and (C-level) path.expand() re-entrantly).

  INSTALLATION and INCLUDED SOFTWARE:



  PACKAGE INSTALLATION:

The new field SysDataCompression in the DESCRIPTION file allows user
      control over the compression used for sysdata.rda objects in the
      lazy-load database.

install.packages(dependencies = value) for value = NA (the default) or
      value = TRUE omits packages only in LinkingTo for binary package
      installs.

  C-LEVEL FACILITIES:

The long undocumented remapping of rround() to Rf_fround() in header
      Rmath.h is now formally deprecated: use fround() directly.

Remapping of prec() and trunc() in the Rmath.h header has been disabled
      in C++ code (it has caused breakage with libc++ headers).

  BUG FIXES:

getParseData() truncated the imaginary part of complex number
      constants.  (Reported by Yihui Xie.)

dbeta(x, a, b) with a or b within a factor of 2 of the largest
      representable number could infinite-loop.  (Reported by Ioannis
      Kosmidis.)

provideDimnames() failed for arrays with a 0 dimension. (PR#15465)

rbind() and cbind() did not handle list objects correctly. (PR#15468)

replayPlot() now checks if it is replaying a plot from the same
      session.

rasterImage() and grid.raster() now give error on an empty
      (zero-length) raster.  (Reported by Ben North.)

plot.lm() would sometimes scramble the labels in plot type 5.
      (PR#15458 and PR#14837)

min() did not handle NA_character_ values properly.  (Reported by
      Magnus Thor Torfason.)

(Windows only.)  readRegistry() would duplicate default values for
      keys.  (PR#15455)

str(..., strict.width = "cut") did not handle it properly when more
      than one line needed to be cut.  (Reported by Gerrit Eichner.)

Removing subclass back-references when S4 classes were removed or their
      namespace unloaded had several bugs (e.g., PR#15481).

aggregate() could fail when there were too many levels present in the
      by argument.  (PR#15004)

namespaceImportFrom() needed to detect primitive functions when
      checking for duplicated imports (reported by Karl Forner).

getGraphicsEvent() did not exit when a user closed the graphics window.
      (PR#15208)

Errors in vignettes were not always captured and displayed properly.
      (PR#15495)

contour() could fail when dealing with extremely small z values.
      (PR#15454)

Several functions did not handle zero-length vectors properly,
      including browseEnv(), format(), gl(), relist() and
      summary.data.frame().  (E.g., PR#15499)

Sweave() did not restore the R output to the console if it was
      interrupted by a user in the middle of evaluating a code chunk.
      (Reported by Michael Sumner.)

Fake installs of packages with vignettes work again.

Illegal characters in the input caused parse() (and thus source()) to
      segfault.  (PR#15518)

The nonsensical use of nmax = 1 in duplicated() or unique() is now
      silently ignored.

qcauchy(p, *) is now fully accurate even when p is very close to 1.
      (PR#15521)

The validmu() and valideta() functions in the standard glm() families
      now also report non-finite values, rather than failing.

Saved vignette results (in a .Rout.save file) were not being compared
      to the new ones during R CMD check.

Double-clicking outside of the list box (e.g., on the scrollbar) of a
      Tk listbox widget generated by tk_select.list() no longer causes
      the window to close. (PR#15407)

Improved handling of edge cases in parallel::splitindices(). (PR#15552)

HTML display of results from help.search() and ?? sometimes contained
      badly constructed links.

c() and related functions such as unlist() converted raw vectors to
      invalid logical vectors. (PR#15535)

(Windows only) When a call to system2() specified one of stdin, stdout
      or stderr to be a file, but the command was not found (e.g., it
      contained its arguments, or the program was not on the PATH), it
      left the file open and unusable until R terminated.  (Reported by
      Mathew McLean.)

The bmp() device was not recording res = NA correctly: it is now
      recorded as 72 ppi.

Several potential problems with compiler-specific behaviour

hcl() now honours NA inputs (previously they were mapped to black).

Some translations in base packages were being looked up in the main
      catalog rather than that for the package.



rowsum() has more support for matrices and dataframes with 2^31 or more
      elements. (PR#15587)

predict(<lm object>, interval = "confidence", scale = <something>) now
      works.  (PR#15564)

The bug fix in 3.0.2 for PR#15411 was too aggressive, and sometimes
      removed spaces that should not have been removed.  (PR#15583)

Running R code in a tcltk callback failed to set the

The code for date-times before 1902 assumed that the offset from GMT in
      1902 was a whole number of minutes: that was not true of Paris
      (as recorded on some platforms).

Using Sys.setlocale to set LC_NUMERIC to "C" (to restore the sane
      behavior) no longer gives a warning.

deparse() now deparses complex vectors in a way that re-parses to the
      original values.  (PR#15534, patch based on code submitted by
      Alex Bertram.)

In some extreme cases (more than 10^15) integer inputs to dpqrxxx()
      functions might have been rounded up by one (with a warning about
      being non-integer).  (PR#15624)

Plotting symbol pch = 14 had the triangle upside down on some devices
      (typically screen devices). The triangle is supposed to be point
      up.  (Reported by Bill Venables.)

getSrcref() did not work on method definitions if rematchDefinition()
      had been used.

KalmanForecast(fast = FALSE) reported a (harmless) stack imbalance.

The count of observations used by KalmanRun() did not take missing
      values into account.

In locales where the abbreviated name of one month is a partial match
      for the full name of a later one, the %B format in strptime()
      could fail.  An example was French on OS X, where juin is
      abbreviated to jui and partially matches juillet.  Similarly for
      weekday names.

pbeta(x, a, b, log.p = TRUE) sometimes underflowed to zero for very
      small and very differently sized a, b.  (PR#15641)

approx() and approxfun() now handle infinite values with the "constant"
      method. (PR#15655)

stripchart() again respects reversed limits in xlim and ylim.
      (PR#15664)

CHANGES IN R 3.0.2:

  NEW FEATURES:

The NEWS files have been re-organized.

      This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y
      and 2.x.y releases is in files NEWS.0, NEWS.1 and NEWS.2.  The
      latter files are now installed when R is installed.  An HTML
      version of news from 2.10.0 to 2.15.3 is available as
      doc/html/NEWS.2.html.

sum() for integer arguments now uses an integer accumulator of at least
      64 bits and so will be more accurate in the very rare case that a
      cumulative sum exceeds 2^53 (necessarily summing more than 4
      million elements).

The example() and tools::Rd2ex() functions now have parameters to allow
      them to ignore \dontrun markup in examples.  (Suggested by Peter
      Solymos.)

str(x) is considerably faster for very large lists, or factors with
      100,000 levels, the latter as in PR#15337.

col2rgb() now converts factors to character strings not integer codes
      (suggested by Bryan Hanson).

tail(warnings()) now works, via the new `[` method.

There is now support for the LaTeX style file zi4.sty which has in some
      distributions replaced inconsolata.sty.



The tools::getVignetteInfo() function has been added to give
      information about installed vignettes.

New assertCondition(), etc. utilities in tools, useful for testing.

Profiling now records non-inlined calls from byte-compiled code to
      BUILTIN functions.

Various functions in stats and elsewhere that use non-standard
      evaluation are now more careful to follow the namespace scoping
      rules.  E.g., stats::lm() can now find stats::model.frame() even
      if stats is not on the search path or if some package defines a
      function of that name.

If an invalid/corrupt .Random.seed object is encountered in the
      workspace it is ignored with a warning rather than giving an
      error.  (This allows R itself to rely on a working RNG, e.g. to
      choose a random port.)

seq() and seq.int() give more explicit error messages if called with
      invalid (e.g., NaN) inputs.

When parse() finds a syntax error, it now makes partial parse
      information available up to the location of the error.  (Request
      of Reijo Sund.)

Methods invoked by NextMethod() had a different dynamic parent to the
      generic. This was causing trouble where S3 methods invoked via
      lazy evaluation could lose track of their generic.  (PR#15267)

Code for the negative binomial distribution now treats the case size ==
      0 as a one-point distribution at zero.

abbreviate() handles without warning non-ASCII input strings which
      require no abbreviation.

read.dcf() no longer has a limit of 8191 bytes per line. (Wish of
      PR#15250.)

formatC(x) no longer copies the class of x to the result, to avoid
      misuse creating invalid objects as in PR#15303.  A warning is
      given if a class is discarded.

Dataset npk has been copied from MASS to allow more tests to be run
      without recommended packages being installed.

The initialization of the regression coefficients for non-degenerate
      differenced models in arima() has been changed and in some
      examples avoids a local maximum.  (PR#15396)

termplot() now has an argument transform.x to control the display of
      individual terms in the plot.  (PR#15329)

format() now supports digits = 0, to display nsmall decimal places.

There is a new read-only par() parameter called "page", which returns a
      logical value indicating whether the next plot.new() call will
      start a new page.

Processing Sweave and Rd documents to PDF now renders backticks and
      single quotes better in several instances, including in \code and
      \samp expressions.

utils::modifyList() gets a new argument keep.null allowing NULL
      components in the replacement to be retained, instead of causing
      corresponding components to be deleted.

tools::pkgVignettes() gains argument check; if set to TRUE, it will
      warn when it appears a vignette requests a non-existent vignette
      engine.

  UTILITIES:

R CMD check --as-cran checks the line widths in usage and examples
      sections of the package Rd files.

R CMD check --as-cran now implies --timings.

R CMD check looks for command gfile if a suitable file is not found.
      (Although file is not from GNU, OpenCSW on Solaris installs it as
      gfile.)

R CMD build (with the internal tar) checks the permissions of configure
      and cleanup files and adds execute permission to the recorded
      permissions for these files if needed, with a warning.  This is
      useful on OSes and file systems which do not support execute
      permissions (notably, on Windows).

R CMD build now weaves and tangles all vignettes, so suggested packages
      are not required during package installation if the source
      tarball was prepared with current R CMD build.

checkFF() (used by R CMD check) does a better job of detecting calls
      from other packages, including not reporting those where a
      function has been copied from another namespace (e.g., as a
      default method).  It now reports calls where .NAME is a symbol
      registered in another package.

On Unix-alike systems, R CMD INSTALL now installs packages group
      writably whenever the library (lib.loc) is group writable.
      Hence, update.packages() works for other group members (suggested
      originally and from a patch by Dirk Eddelbuettel).

R CMD javareconf now supports the use of symbolic links for JAVA_HOME
      on platforms which have realpath.  So it is now possible to use
      
      R CMD javareconf JAVA_HOME=/usr/lib/jvm/java-1.7.0

      on a Linux system and record that value rather than the
      frequently-changing full path such as
      /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25.x86_64.

(Windows only.) Rscript -e requires a non-empty argument for
      consistency with Unix versions of R.  (Also Rterm -e and R -e.)

R CMD check does more thorough checking of declared packages and
      namespaces.  It reports

packages declared in more than one of the Depends, Imports, Suggests
          and Enhances fields of the DESCRIPTION file.

namespaces declared in Imports but not imported from, neither in the
          NAMESPACE file nor using the :: nor ::: operators.

packages which are used in library() or requires() calls in the R code
          but were already put on the search path _via_ Depends.

packages declared in Depends not imported _via_ the NAMESPACE file
          (except the standard packages).  Objects used from Depends
          packages should be imported to avoid conflicts and to allow
          correct operation when the namespace is loaded but not
          attached.

objects imported _via_ ::: calls where :: would do.

objects imported by :: which are not exported.

objects imported by ::: calls which do not exist.


R CMD check optionally checks for non-standard top-level files and
      directories (which are often mistakes): this is enabled for
      --as-cran.

LaTeX style file upquote.sty is no longer included (the version was
      several years old): it is no longer used in R.  A much later
      version is commonly included in LaTeX distributions but does not
      play well with the ae fonts which are the default for Sweave
      vignettes.

R CMD build makes more use of the build sub-directory of package
      sources, for example to record information about the vignettes.

R CMD check analyses ::: calls.

  INSTALLATION and INCLUDED SOFTWARE:

The macros used for the texinfo manuals have been changed to work
      better with the incompatible changes made in texinfo 5.x.

The minimum version for a system xz library is now 5.0.3 (was 4.999).
      This is in part to avoid 5.0.2, which can compress in ways other
      versions cannot decompress.

The included version of PCRE has been updated to 8.33.

The included version of zlib has been updated to 1.2.8, a bug-fix
      release.

The included version of xz utils's liblzma has been updated to 5.0.5.

Since javareconf (see above) is used when R is installed, a stable link
      for JAVA_HOME can be supplied then.

Configuring with --disable-byte-compilation will override the
      DESCRIPTION files of recommended packages, which typically
      require byte-compilation.

More of the installation and checking process will work even when
      TMPDIR is set to a path containing spaces, but this is not
      recommended and external software (such as texi2dvi) may fail.

  PACKAGE INSTALLATION:

Installation is aborted immediately if a LinkingTo package is not
      installed.

R CMD INSTALL has a new option --no-byte-compile which will override a
      ByteCompile field in the package's DESCRIPTION file.

License BSD is deprecated: use BSD_3_clause or BSD_2_clause instead.

      License X11 is deprecated: use MIT or BSD_2_clause instead.

Version requirements for LinkingTo packages are now recognized: they
      are checked at installation.  (Fields with version requirements
      were previously silently ignored.)

The limit of 500 S3method entries in a NAMESPACE file has been removed.



  C-LEVEL FACILITIES:

Rdefines.h has been tweaked so it can be included in C++ code after
      R_ext/Boolean.h (which is included by R.h).

      Note that Rdefines.h is not kept up-to-date, and Rinternals.h is
      preferred for new code.

eval and applyClosure are now protected against package code supplying
      an invalid rho.

  DEPRECATED AND DEFUNCT:

The unused namespace argument to package.skeleton() is now formally
      deprecated and will be removed in R 3.1.0.

plclust() is deprecated: use the plot() method for class "hclust"
      instead.

Functions readNEWS() and checkNEWS() in package tools are deprecated
      (and they have not worked with current NEWS files for a long
      time).

  DOCUMENTATION:



  BUG FIXES:

help.request() could not determine the current version of R on CRAN.
      (PR#15241)

On Windows, file.info() failed on root directories unless the path was
      terminated with an explicit ".".  (PR#15302)

The regmatches<-() replacement function mishandled results coming from
      regexpr().  (PR#15311)

The help for setClass() and representation() still suggested the
      deprecated argument representation=. (PR#15312)

R CMD config failed in an installed build of R 3.0.1 (only) when a
      sub-architecture was used.  (Reported by Berwin Turlach.)

On Windows, the installer modified the etc/Rconsole and
      etc/Rprofile.site files even when default options were chosen, so
      the MD5 sums did not refer to the installed versions.  (Reported
      by Tal Galili.)

plot(hclust(), cex =) respects cex again (and possibly others
      similarly).  (Reported by Peter Langfelder.)

If multiple packages were checked by R CMD check, and one was written
      for a different OS, it would set --no-install for all following
      packages as well as itself.

qr.coef() and related functions did not properly coerce real vectors to
      complex when necessary.  (PR#15332)

ftable(a) now fixes up empty dimnames such that the result is
      printable.

package.skeleton() was not starting its search for function objects in
      the correct place if environment was supplied.  (Reported by Karl
      Forner.)

Parsing code was changing the length field of vectors and confusing the
      memory manager.  (PR#15345)

The Fortran routine ZHER2K in the reference BLAS had a comment-out bug
      in two places.  This caused trouble with eigen() for Hermitian
      matrices.  (PR#15345 and report from Robin Hankin)

vignette() and browseVignettes() did not display non-Sweave vignettes
      properly.

Two warning/error messages have been corrected: the (optional) warning
      produced by a partial name match with a pairlist, the error
      message from a zero-length argument to the : operator.  (Found by
      Radford Neal; PR#15358, PR#15356)

svd() returned NULL rather than omitting components as documented.
      (Found by Radford Neal; PR#15360)

mclapply() and mcparallel() with silent = TRUE could break a process
      that uses stdout output unguarded against broken pipes (e.g., zip
      will fail silently). To work around such issues, they now replace
      stdout with a descriptor pointed to /dev/null instead. For this
      purpose, internal closeStdout and closeStderr functions have
      gained the to.null flag.

log(), signif() and round() now raise an error if a single named
      argument is not named x.  (PR#15361)

deparse() now deparses raw vectors in a form that is syntactically
      correct. (PR#15369)

The jpeg driver in Sweave created a JPEG file, but gave it a .png
      extension. (PR#15370)

Deparsing of infix operators with named arguments is improved.
      (PR#15350)

mget(), seq.int() and numericDeriv() did not duplicate arguments
      properly. (PR#15352, PR#15353, PR#15354)

kmeans(algorithm = "Hartigan-Wong") now always stops iterating in the
      QTran stage. (PR#15364).

read.dcf() re-allocated incorrectly and so could segfault when called
      on a file with lines of more than 100 bytes.

On systems where mktime() does not set errno, the last second before
      the epoch could not be converted from POSIXlt to POSIXct.
      (Reported by Bill Dunlap.)

add1.glm() miscalculated F-statistics when df > 1. (Bill Dunlap,
      PR#15386).

stem() now discards infinite inputs rather than hanging.  (PR#15376)

The parser now enforces C99 syntax for floating point hexadecimal
      constants (e.g., 0x1.1p0), rather than returning unintended
      values for malformed constants. (PR#15234)

model.matrix() now works with very long LHS names (more than 500
      bytes).  (PR#15377)

integrate() reverts to the pre-2.12.0 behaviour: from 2.12.0 to 3.0.1
      it sometimes failed to achieve the requested tolerance and
      reported error estimates that were exceeded.  (PR#15219)

strptime() now handles %W fields with value 0. (PR#15915)

R is now better protected against people trying to interact with the
      console in startup code.  (PR#15325)

Subsetting 1D arrays often lost dimnames (PR#15301).

Unary + on a logical vector did not coerce to integer, although unary -
      did.

na.omit() and na.exclude() added a row to a zero-row data frame.
      (PR#15399)

All the (where necessary cut-down) vignettes are installed if R was
      configured with --without-recommended-packages.

source() did not display filenames when reporting syntax errors.

Syntax error reports misplaced the caret pointing out the bad token.

(Windows only) Starting R with R (instead of Rterm or Rgui) would lose
      any zero-length strings from the command line arguments.
      (PR#15406)

Errors in the encoding specified on the command line via --encoding=foo
      were not handled properly.  (PR#15405)

If x is a symbol, is.vector(x, "name") now returns TRUE, since "name"
      and "symbol"

R CMD rtags works on platforms (such as OS X) with a XSI-conformant
      shell command echo. (PR#15231)

is.unsorted(NA) returns false as documented (rather than NA).

R CMD LINK did not know about sub-architectures.

system() and system2() are better protected against users who
      misguidedly have spaces in the temporary directory path.

file.show() and edit() are now more likely to work on file paths
      containing spaces.  (Where external utilities are used, not the
      norm on Windows nor in R.app which should previously have
      worked.)

Packages using the methods package are more likely to work when they
      import it but it is not attached.  (Several parts of its C code
      were looking for its R functions on the search path rather than
      in its namespace.)

lgamma(-x) is no longer NaN for very small x.

(Windows) system2() now respects specifying stdout and stderr as files
      if called from Rgui. (PR#15393)

Closing an x11() device whilst locator() or identify() is in progress
      no longer hangs R.  (PR#15253)

list.dirs(full.names = FALSE) was not implemented.  (PR#15170)

format() sometimes added unnecessary spaces.  (PR#15411)

all.equal(check.names = FALSE) would ignore the request to ignore the
      names and would check them as attributes.

The symbol set by tools::Rd2txt_options(itemBullet=) was not respected
      in some locales. (PR#15435)

mcMap() was not exported by package parallel. (PR#15439)

plot() for TukeyHSD objects did not balance dev.hold() and dev.flush()
      calls on multi-page plots.  (PR#15449)

CHANGES IN R 3.0.1:

  NEW FEATURES:

chooseCRANmirror() and chooseBioCmirror() gain an ind argument (like
      setRepositories()).

mcparallel has a new argument mc.interactive which can modify the
      interactive flag in the child process. The new default is FALSE
      which makes child processes non-interactive by default (this
      prevents lock-ups due to children waiting for interactive input).

scan() now warns when end-of-file occurs within a quoted string.

count.fields() is now consistent with scan() in its handling of
      newlines in quoted strings.  Instead of triggering an error, this
      results in the current line receiving NA as the field count, with
      the next line getting the total count of the two lines.

The default method of image() will plot axes of the class of xlim and
      ylim (and hence of x and y if there is a suitable range()
      method).  Based on a suggestion of Michael Sumner.

load() now has a verbose argument for debugging support, to print the
      names of objects just before loading them.

When loading a serialized object encounters a reference to a namespace
      which cannot be loaded, this is replaced by a reference to the
      global environment, with a warning.

pairs() gains a line.main option for title placement.

The remaining instances in which serialization to a raw vector was
      limited to 2GB have been unlimited on a 64-bit platform, and in
      most cases serialization to a vector of more than 1GB will be
      substantially faster.

  UTILITIES:

R CMD config now make use of personal Makevars files under ~/.R and a
      site file Makevars.site, in the same way as R CMD SHLIB and R CMD
      INSTALL.  This makes the utility more useful in package configure
      scripts.

      On Windows finding the personal files may require the environment
      variable HOME set.

      The old behaviour can be obtained with the new options
      --no-user-files and --no-site-files.

  PACKAGE INSTALLATION:

Alternatives to the site and user customization files Makevars.site and
      ~/.R/Makevars can be specified _via_ the environment variables
      R_MAKEVARS_SITE and R_MAKEVARS_USER respectively.  These can be
      used to suppress the use of the default files by setting an empty
      value (where possible) or a non-existent path.

  BUG FIXES:

sys.source() did not report error locations when keep.source = TRUE.

as.POSIXct.numeric was coercing origin using the tz argument and not
      "GMT" as documented (PR#14973).

The active binding to assign fields in reference classes has been
      cleaned up to reduce dependence on the class' package
      environment, also fixing bug in initializing read-only fields
      (inspired by a report from Hadley Wickham).

str(d) no longer gives an error when names(d) contain illegal multibyte
      strings (PR#15247).

Profiling of built-in functions with line.profiling= TRUE did not
      record the line from which they were called.

citation(pkg) dropped the header and footer specified in the CITATION
      file (PR#15257).

Quotes were handled differently when reading the first line and reading
      the rest, so read.table() misread some files that contained quote
      characters (PR#15245).

cat() with sep a character vector of length greater than one and more
      than one argument was using separators inconsistently (PR#15261).

On Windows in R 3.0.0, savePlot() failed because of an incorrect check
      on the argument count.

unzip(list = TRUE) returned Names as a factor and not a character
      vector (as documented) for the internal method.  (Noticed by Sean
      O'Riordain.)

contourLines() now checks more comprehensively for conformance of its
      x, y and z arguments (it was used incorrectly in package R2G2).

Saved graphics display lists are R version-specific.  Attempting to
      load workspaces containing them (or some other version-specific
      objects) aborted the load in R 3.0.0 and earlier; now it does a
      partial load and generates a warning instead.

In R 3.0.0, identify() and locator() did not record information
      correctly, so replaying a graph (e.g., by copying it to another
      device) would fail. (PR#15271)

Calling file.copy() or dirname() with the invalid input "" (which was
      being used in packages, despite not being a file path) could have
      caused a segfault.

      dirname("") is now "" rather than "." (unless it segfaulted).

supsmu() could read/write outside its input vectors for very short
      inputs (seen in package rms for n = 4).

as.dendrogram()'s hclust method uses less memory and hence gets
      considerably faster for large (n ~ 1000)

The return value when all workers failed from
      parallel::mclapply(mc.preschedule = TRUE) was a list of strings
      and not of error objects.  (Spotted by Karl Forner and Bernd
      Bischl.)

In R 3.0.0, when help() found multiple pages with the same alias, the
      HTML display of all the selections was not produced.  (PR#15282)

splinefun(method="monoH.FC") now produces a function with first
      argument named x and allows deriv=3, as documented. (PR#15273)

summaryRprof() would only read the first chunksize lines of an Rprof
      file produced with line.profiling=TRUE. By default, this is the
      first 100 seconds.  (PR#15288)

lsfit() produced an incorrect error message when argument x had more
      columns than rows or x had a different number of rows than y.
      (Spotted by Renaud Gaujoux.)

Binary operations on equal length vectors copied the class name from
      the second operand when the first had no class name, but did not
      set the object bit. (PR#15299)

The trace() method for reference generator objects failed after those
      objects became function definitions.

write.table() did not check that factors were constructed correctly,
      and so caused a segment fault when writing bad ones. (PR#15300)

The internal HTTP server no longer chokes on POST requests without
      body. It will also pass-through other request types for custom
      handlers (with the method stored in Request-Method header)
      instead of failing.

CHANGES IN R 3.0.0:

  SIGNIFICANT USER-VISIBLE CHANGES:

Packages need to be (re-)installed under this version (3.0.0) of R.

There is a subtle change in behaviour for numeric index values 2^31 and
      larger.  These never used to be legitimate and so were treated as
      NA, sometimes with a warning.  They are now legal for long
      vectors so there is no longer a warning, and x[2^31] <- y will
      now extend the vector on a 64-bit platform and give an error on a
      32-bit one.

It is now possible for 64-bit builds to allocate amounts of memory
      limited only by the OS.  It may be wise to use OS facilities
      (e.g., ulimit in a bash shell, limit in csh), to set limits on
      overall memory consumption of an R process, particularly in a
      multi-user environment.  A number of packages need a limit of at
      least 4GB of virtual memory to load.

      64-bit Windows builds of R are by default limited in memory usage
      to the amount of RAM installed: this limit can be changed by
      command-line option --max-mem-size or setting environment
      variable R_MAX_MEM_SIZE.

Negative numbers for colours are consistently an error: previously they
      were sometimes taken as transparent, sometimes mapped into the
      current palette and sometimes an error.

  NEW FEATURES:

identical() has a new argument, ignore.environment, used when comparing
      functions (with default FALSE as before).

There is a new option, options(CBoundsCheck=), which controls how .C()
      and .Fortran() pass arguments to compiled code.  If true (which
      can be enabled by setting the environment variable
      R_C_BOUNDS_CHECK to yes), raw, integer, double and complex
      arguments are always copied, and checked for writing off either
      end of the array on return from the compiled code (when a second
      copy is made).  This also checks individual elements of character
      vectors passed to .C().

      This is not intended for routine use, but can be very helpful in
      finding segfaults in package code.

In layout(), the limits on the grid size have been raised (again).

New simple provideDimnames() utility function.

Where methods for length() return a double value which is representable
      as an integer (as often happens for package Matrix), this is
      converted to an integer.

Matrix indexing of dataframes by two-column numeric indices is now
      supported for replacement as well as extraction.

setNames() now has a default for its object argument, useful for a
      character result.

StructTS() has a revised additive constant in the loglik component of
      the result: the previous definition is returned as the loglik0
      component.  However, the help page has always warned of a lack of
      comparability of log-likelihoods for non-stationary models.
      (Suggested by Jouni Helske.)

The logic in aggregate.formula() has been revised.  It is now possible
      to use a formula stored in a variable; previously, it had to be
      given explicitly in the function call.

install.packages() has a new argument quiet to reduce the amount of
      output shown.

Setting an element of the graphics argument lwd to a negative or
      infinite value is now an error.  Lines corresponding to elements
      with values NA or NaN are silently omitted.

      Previously the behaviour was device-dependent.

Setting graphical parameters cex, col, lty, lwd and pch in par() now
      requires a length-one argument.  Previously some silently took
      the first element of a longer vector, but not always when
      documented to do so.

Sys.which() when used with inputs which would be unsafe in a shell
      (e.g., absolute paths containing spaces) now uses appropriate
      quoting.

as.tclObj() has been extended to handle raw vectors.  Previously, it
      only worked in the other direction.  (Contributed by Charlie
      Friedemann, PR#14939.)

New functions cite() and citeNatbib() have been added, to allow
      generation of in-text citations from "bibentry" objects.  A
      cite() function may be added to bibstyle() environments.

A sort() method has been added for "bibentry" objects.

The bibstyle() function now defaults to setting the default
      bibliography style. The getBibstyle() function has been added to
      report the name of the current default style.

scatter.smooth() now has an argument lpars to pass arguments to
      lines().

pairs() has a new log argument, to allow some or all variables to be
      plotted on logarithmic scale.  (In part, wish of PR#14919.)

split() gains a sep argument.

termplot() does a better job when given a model with interactions (and
      no longer attempts to plot interaction terms).

The parser now incorporates code from Romain Francois' parser package,
      to support more detailed computation on the code, such as syntax
      highlighting, comment-based documentation, etc.  Functions
      getParseData() and getParseText() access the data.

There is a new function rep_len() analogous to rep.int() for when speed
      is required (and names are not).

The undocumented use rep(NULL, length.out = n) for n > 0 (which returns
      NULL) now gives a warning.

demo() gains an encoding argument for those packages with non-ASCII
      demos: it defaults to the package encoding where there is one.

strwrap() converts inputs with a marked encoding to the current locale:
      previously it made some attempt to pass through as bytes inputs
      invalid in the current locale.

Specifying both rate and scale to [dpqr]gamma is a warning (if they are
      essentially the same value) or an error.

merge() works in more cases where the data frames include matrices.
      (Wish of PR#14974.)

optimize() and uniroot() no longer use a shared parameter object across
      calls.  (nlm(), nlminb() and optim() with numerical derivatives
      still do, as documented.)

The all.equal() method for date-times is now documented: times are
      regarded as equal (by default) if they differ by up to 1 msec.

duplicated() and unique() gain a nmax argument which can be used to
      make them much more efficient when it is known that there are
      only a small number of unique entries.  This is done
      automatically for factors.

Functions rbinom(), rgeom(), rhyper(), rpois(), rnbinom(), rsignrank()
      and rwilcox() now return integer (not double) vectors.  This
      halves the storage requirements for large simulations.

sort(), sort.int() and sort.list() now use radix sorting for factors of
      less than 100,000 levels when method is not supplied.  So does
      order() if called with a single factor, unless na.last = NA.

diag() as used to generate a diagonal matrix has been re-written in C
      for speed and less memory usage.  It now forces the result to be
      numeric in the case diag(x) since it is

backsolve() (and forwardsolve()) are now internal functions, for speed
      and support for large matrices.

More matrix algebra functions (e.g., chol() and solve()) accept logical
      matrices (and coerce to numeric).

sample.int() has some support for n >= 2^31: see its help for the
      limitations.

      A different algorithm is used for (n, size, replace = FALSE, prob
      = NULL) for n > 1e7 and size <= n/2.  This is much faster and
      uses less memory, but does give different results.

approxfun() and splinefun() now return a wrapper to an internal
      function in the stats namespace rather than a .C() or .Call()
      call.  This is more likely to work if the function is saved and
      used in a different session.

The functions .C(), .Call(), .External() and .Fortran() now give an
      error (rather than a warning) if called with a named first
      argument.

Sweave() by default now reports the locations in the source file(s) of
      each chunk.

clearPushBack() is now a documented interface to a long-existing
      internal call.

aspell() gains filters for R code, Debian Control Format and message
      catalog files, and support for R level dictionaries.  In
      addition, package utils now provides functions
      aspell_package_R_files() and aspell_package_C_files() for spell
      checking R and C level message strings in packages.



gray() and gray.colors() finally allow alpha to be specified.

monthplot() gains parameters to control the look of the reference
      lines.  (Suggestion of Ian McLeod.)

Added support for new %~% relation

domain = NA is accepted by gettext() and ngettext(), analogously to
      stop() etc.

termplot() gains a new argument plot = FALSE which returns information
      to allow the plots to be modified for use as part of other plots,
      but does not plot them.  (Contributed by Terry Therneau,
      PR#15076.)

quartz.save(), formerly an undocumented part of R.app, is now available
      to copy a device to a quartz() device.  dev.copy2pdf() optionally
      does this for PDF output: quartz.save() defaults to PNG.

The default method of pairs() now allows text.panel = NULL and the use
      of <foo>.panel = NULL is now documented.

setRefClass() and getRefClass() now return class generator functions,
      similar to setClass(), but still with the reference fields and
      methods as before (suggestion of Romain Francois).

New functions bitwNot(), bitwAnd(), bitwOr() and bitwXor(), using the
      internal interfaces previously used for classes "octmode" and
      "hexmode".

      Also bitwShiftL() and bitwShiftR() for shifting bits in elements
      of integer vectors.

New option "deparse.cutoff" to control the deparsing of language
      objects such as calls and formulae when printing.  (Suggested by
      a comment of Sarah Goslee.)

colors() gains an argument distinct.

New demo(colors) and demo(hclColors), with utility functions.

list.files() (aka dir()) gains a new optional argument no.. which
      allows to exclude "." and ".." from listings.

Multiple time series are also of class "matrix"; consequently, head(),
      e.g., is more useful.

encodeString() preserves UTF-8 marked encodings.  Thus if factor levels
      are marked as UTF-8 an attempt is made to print them in UTF-8 in
      RGui on Windows.

readLines() and scan() (and hence read.table()) in a UTF-8 locale now
      discard a UTF-8 byte-order-mark (BOM).  Such BOMs are allowed but
      not recommended by the Unicode Standard: however Microsoft
      applications can produce them and so they are sometimes found on
      websites.

      The encoding name "UTF-8-BOM" for a connection will ensure that a
      UTF-8 BOM is discarded.

mapply(FUN, a1, ..) now also works when a1 (or a further such argument)
      needs a length() method (which the

.onDetach() is supported as an alternative to .Last.lib.  Unlike
      .Last.lib, this does not need to be exported from the package's
      namespace.

The srcfile argument to parse() may now be a character string, to be
      used in error messages.

The format() method for ftable objects gains a method argument,
      propagated to write.ftable() and print(), allowing more compact
      output, notably for LaTeX formatting, thanks to Marius Hofert.

The utils::process.events() function has been added to trigger
      immediate event handling.

Sys.which() now returns NA (not "") for NA inputs (related to
      PR#15147).

The print() method for class "htest" gives fewer trailing spaces (wish
      of PR#15124).

      Also print output from HoltWinters(), nls() and others.

loadNamespace() allows a version specification to be given, and this is
      used to check version specifications given in the Imports field
      when a namespace is loaded.

setClass() has a new argument, slots, clearer and less ambiguous than
      representation.  It is recommended for future code, but should be
      back-compatible.  At the same time, the allowed slot
      specification is slightly more general.  See the documentation
      for details.

mget() now has a default for envir (the frame from which it is called),
      for consistency with get() and assign().

close() now returns an integer status where available, invisibly. (Wish
      of PR#15088.)

The internal method of tar() can now store paths too long for the ustar
      format, using the (widely supported) GNU extension.  It can also
      store long link names, but these are much less widely supported.
      There is support for larger files, up to the ustar limit of 8GB.

Local reference classes have been added to package methods.  These are
      a technique for avoiding unneeded copying of large components of
      objects while retaining standard R functional behavior.  See
      ?LocalReferenceClasses.

untar() has a new argument restore_times which if false (not the
      default) discards the times in the tarball.  This is useful if
      they are incorrect (some tarballs submitted to CRAN have times in
      a local time zone or many years in the past even though the
      standard required them to be in UTC).

replayplot() cannot (and will not attempt to) replay plots recorded
      under R < 3.0.0.  It may crash the R session if an attempt is
      made to replay plots created in a different build of R >= 3.0.0.

Palette changes get recorded on the display list, so replaying plots
      (including when resizing screen devices and using dev.copy())
      will work better when the palette is changed during a plot.

chol(pivot = TRUE) now defaults to LAPACK, not LINPACK.

The parse() function has a new parameter keep.source, which defaults to
      options("keep.source").

Profiling via Rprof() now optionally records information at the
      statement level, not just the function level.

The Rprof() function now quotes function names in in its output file on
      Windows, to be consistent with the quoting in Unix.

Profiling via Rprof() now optionally records information about time
      spent in GC.

The HTML help page for a package now displays non-vignette
      documentation files in a more accessible format.

To support options(stringsAsFactors = FALSE), model.frame(),
      model.matrix() and replications() now automatically convert
      character vectors to factors without a warning.

The print method for objects of class "table" now detects tables with
      0-extents and prints the results as, e.g., < table of extent 0 x
      1 x 2 >. (Wish of PR#15198.)

Deparsing involving calls to anonymous functions has been made closer
      to reversible by the addition of extra parentheses.

The function utils::packageName() has been added as a lightweight
      version of methods::getPackageName().

find.package(lib.loc = NULL) now treats loaded namespaces
      preferentially in the same way as attached packages have been for
      a long time.

In Windows, the Change Directory dialog now defaults to the current
      working directory, rather than to the last directory chosen in
      that dialog.

available.packages() gains a "license/restricts_use" filter which
      retains only packages for which installation can proceed solely
      based on packages which are guaranteed not to restrict use.

New check_packages_in_dir() function in package tools for conveniently
      checking source packages along with their reverse dependencies.

R's completion mechanism has been improved to handle help requests
      (starting with a question mark).  In particular, help prefixes
      are now supported, as well as quoted help topics.  To support
      this, completion inside quotes are now handled by R by default on
      all platforms.

The memory manager now allows the strategy used to balance garbage
      collection and memory growth to be controlled by setting the
      environment variable R_GC_MEM_GROW. See ?Memory for more details.



On Windows, the device name for bitmap devices as reported by .Device
      and .Devices no longer includes the file name.  This is for
      consistency with other platforms and was requested by the lattice
      maintainer.

      win.metafile() still uses the file name: the exact form is used
      by package tkrplot.

set.seed(NULL) re-initializes .Random.seed as done at the beginning of
      the session if not already set.  (Suggestion of Bill Dunlap.)

The breaks argument in hist.default() can now be a function that
      returns the breakpoints to be used (previously it could only
      return the suggested number of breakpoints).

File share/licenses/licenses.db has some

  LONG VECTORS:

  This section applies only to 64-bit platforms.

There is support for vectors longer than 2^31 - 1 elements.  This
      applies to raw, logical, integer, double, complex and character
      vectors, as well as lists.  (Elements of character vectors remain
      limited to 2^31 - 1 bytes.)



length() returns a double for long vectors, and lengths can be set to
      2^31 or more by the replacement function with a double value.

Most aspects of indexing are available.  Generally double-valued
      indices can be used to access elements beyond 2^31 - 1.

There is some support for matrices and arrays with each dimension less
      than 2^31 but total number of elements more than that.  Only some
      aspects of matrix algebra work for such matrices, often taking a
      very long time.  In other cases the underlying Fortran code has
      an unstated restriction (as was found for complex svd()).

dist() can produce dissimilarity objects for more than 65536 rows (but
      for example hclust() cannot process such objects).

serialize() to a raw vector is unlimited in size (except by resources).

The C-level function R_alloc can now allocate 2^35 or more bytes.

agrep() and grep() will return double vectors of indices for long
      vector inputs.

Many calls to .C() have been replaced by .Call() to allow long vectors
      to be supported (now or in the future).  Regrettably several
      packages had copied the non-API .C() calls and so failed.

.C() and .Fortran() do not accept long vector inputs.  This is a
      precaution as it is very unlikely that existing code will have
      been written to handle long vectors (and the R wrappers often
      assume that length(x) is an integer).

Most of the methods for sort() work for long vectors.

      rank(), sort.list() and order() support long vectors (slowly
      except for radix sorting).

sample() can do uniform sampling from a long vector.

  PERFORMANCE IMPROVEMENTS:

More use has been made of R objects representing registered entry
      points, which is more efficient as the address is provided by the
      loader once only when the package is loaded.

      This has been done for packages base, methods, splines and tcltk:
      it was already in place for the other standard packages.

      Since these entry points are always accessed by the R entry
      points they do not need to be in the load table which can be
      substantially smaller and hence searched faster.  This does mean
      that .C / .Fortran / .Call calls copied from earlier versions of
      R may no longer work - but they were never part of the API.

Many .Call() calls in package base have been migrated to .Internal()
      calls.

solve() makes fewer copies, especially when b is a vector rather than a
      matrix.

eigen() makes fewer copies if the input has dimnames.

Most of the linear algebra functions make fewer copies when the
      input(s) are not double (e.g., integer or logical).

A foreign function call (.C() etc) in a package without a PACKAGE
      argument will only look in the first DLL specified in the
      NAMESPACE file of the package rather than searching all loaded
      DLLs.  A few packages needed PACKAGE arguments added.

The @<- operator is now implemented as a primitive, which should reduce
      some copying of objects when used.  Note that the operator object
      must now be in package base: do not try to import it explicitly
      from package methods.

  PACKAGE INSTALLATION:

The transitional support for installing packages without namespaces
      (required since R 2.14.0) has been removed.  R CMD build will
      still add a namespace, but a .First.lib() function will need to
      be converted.

      R CMD INSTALL no longer adds a namespace (so installation will
      fail), and a .First.lib() function in a package will be ignored
      (with an installation warning for now).

      As an exception, packages without a R directory and no NAMESPACE
      file can still be installed.

Packages can specify in their DESCRIPTION file a line like
      
           Biarch: yes

      to be installed on Windows with --force-biarch.



The *.R tangled source code for vignettes is now included in tarballs
      when R CMD build is used to produce them.  In R 3.0.0, *.R files
      not in the sources will be produced at install time, but
      eventually this will be dropped.

The package type "mac.binary" now looks in a path in the repository
      without any Mac subtype (which used to be universal or leopard):
      it looks in bin/macosx/contrib/3.0 rather than
      bin/macosx/leopard/contrib/2.15).  This is the type used for the
      CRAN binary distribution for OS X as from R 3.0.0.

File etc/Makeconf makes more use of the macros $(CC), $(CXX), $(F77)
      and $(FC), so the compiler in use can be changed by setting just
      these (and if necessary the corresponding flags and FLIBS) in
      file ~/.R/Makevars.

      This is convenient for those working with binary distributions of
      R, e.g. on OS X.

  UTILITIES:

R CMD check now gives a warning rather than a note if it finds calls to
      abort, assert or exit in compiled code, and has been able to find
      the .o file in which the calls occur.

      Such calls can terminate the R process which loads the package.

The location of the build and check environment files can now be
      specified by the environment variables R_BUILD_ENVIRON and
      R_CHECK_ENVIRON, respectively.

R CMD Sweave gains a --compact option to control possibly reducing the
      size of the PDF file it creates when --pdf is given.

R CMD build now omits Eclipse's .metadata directories, and R CMD check
      warns if it finds them.

R CMD check now does some checks on functions defined within reference
      classes, including of .Call() etc calls.

R CMD check --as-cran notes assignments to the global environment,
      calls to data() which load into the global environment, and calls
      to attach().

R CMD build by default uses the internal method of tar() to prepare the
      tarball.  This is more likely to produce a tarball compatible
      with R CMD INSTALL and R CMD check: an external tar program,
      including options, can be specified _via_ the environment
      variable R_BUILD_TAR.

tools::massageExamples() is better protected against packages which
      re-define base functions such as cat() and get() and so can cause
      R CMD check to fail when checking examples.

R CMD javareconf has been enhanced to be more similar to the code used
      by configure.

      There is now a test that a JNI program can be compiled (like
      configure did) and only working settings are used.

      It makes use of custom settings from configuration recorded in
      etc/javaconf.

The --no-vignettes argument of R CMD build has been renamed to the more
      accurate --no-build-vignettes: its action has always been to
      (re)build vignettes and never omitted them.

      R CMD check accepts --no-build-vignettes as a preferred synonym
      for --no-rebuild-vignettes.

  DEPRECATED AND DEFUNCT:

The ENCODING argument to .C() is defunct.  Use iconv() instead.

The .Internal(eval.with.vis) non-API function has been removed.

Support for the converters for use with .C() has been removed,
      including the oft misused non-API header R_ext/RConverters.h.

The previously deprecated uses of array() with a 0-length dim argument
      and tapply() with a 0-length INDEX list are now errors.

Translation packages are defunct.

Calling rep() or rep.int() on a pairlist or other non-vector object is
      now an error.

Several non-API entry points have been transferred to packages (e.g.,
      R_zeroin2) or replaced by different non-API entry points (e.g.,
      R_tabulate).



The .Fortran() entry point "dqrls" which has not been used by R since
      version 2.15.1 is no longer available.

Functions traceOn() and traceOff() in package methods are now defunct.

Function CRAN.packages() is finally defunct.

Use of col2rgb(0) is defunct: use par("bg") or NA instead.

The long-defunct functions Rd_parse(), anovalist.lm(), categpry(),
      clearNames(), gammaCody(), glm.fit.null(), lm.fit.null(),
      lm.wfit.null(), manglePackageNames(), mauchley.test(),
      package.contents(), print.coefmat(), reshapeLong(),
      reshapeWide(), tkclose(), tkcmd(), tkfile.dir(), tkfile.tail(),
      tkopen(), tkputs(), tkread(), trySilent() and zip.file.extract()
      have been removed entirely (but are still documented in the help
      system).

The unused dataPath argument to attachNamespace() has been removed.

grid.prompt() has been removed: use devAskNewPage() instead.

The long-deprecated intensities component is no longer returned by
      hist().

mean() for data frames and sd() for data frames and matrices are
      defunct.

chol(pivot = FALSE, LINPACK = TRUE), ch2inv(LINPACK = TRUE),
      eigen(EISPACK = TRUE), solve(LINPACK = TRUE) and svd(LINPACK =
      TRUE) are defunct: LAPACK will be used, with a warning.

The keep.source argument to library() and require() is defunct.  This
      option needs to be set at install time.



The maxRasters argument of pdf() (unused since R 2.14.0) has been
      removed.

The unused fontsmooth argument has been removed from the quartz()
      device.

All the (non-API) EISPACK entry points in R have been removed.

chol(pivot = TRUE, LINPACK = TRUE) is deprecated.

The long-deprecated use of \synopsis in the Usage section of .Rd files
      will be removed in R 3.1.0.

.find.package() and .path.package() are deprecated: only the public
      versions without the dot have ever been in the API.

In a package's DESCRIPTION file,
      
          License: X11

      is deprecated, since it includes

  CODE MIGRATION:

The C code underlying base graphics has been migrated to the graphics
      package (and hence no longer uses .Internal() calls).

Most of the .Internal() calls used in the stats package have been
      migrated to C code in that package.

      This means that a number of .Internal() calls which have been
      used by packages no longer exist, including .Internal(cor)
      .Internal(cov), .Internal(optimhess) and
      .Internal(update.formula).

Some .External() calls to the base package (really to the R executable
      or shared library) have been moved to more appropriate packages.
      Packages should not have been using such calls, but some did
      (mainly those used by integrate()).

  PACKAGE parallel:

There is a new function mcaffinity() which allows getting or setting
      the CPU affinity mask for the current R process on systems that
      supports this (currently only Linux has been tested
      successfully).  It has no effect on systems which do not support
      process affinity.  Users are not expected to use this function
      directly (with the exception of fixing libraries that break
      affinity settings like OpenBLAS) - the function is rather
      intended to support affinity control in high-level parallel
      functions.  In the future, R may supplement lack of affinity
      control in the OS by its own bookkeeping via mcaffinity() related
      to processes and threads it spawns.

mcparallel() has a new argument mc.affinity which attempts to set the
      affinity of the child process according to the specification
      contained therein.

The port used by socket clusters is chosen randomly: this should help
      to avoid clashes observed when two users of a multi-user machine
      try to create a cluster at the same time.  To reproduce the
      previous behaviour set environment variable R_PARALLEL_PORT to
      10187.

  C-LEVEL FACILITIES:

There has been some minor re-organization of the non-API header files.
      In particular, Rinternals.h no longer includes the non-API header
      R_exts/PrtUtil.h, and that no longer includes R_exts/Print.h.

Passing NULL to .C() is now an error.

.C() and .Fortran() now warn if "single" arguments are used with DUP =
      FALSE, as changes to such arguments are not returned to the
      caller.

C entry points R_qsort and R_qsort_I now have start and end as size_t
      to allow them to work with longer vectors on 64-bit platforms.
      Code using them should be recompiled.

A few recently added C entry points were missing the remapping to Rf_,
      notably [dpq]nbinom_mu.

Some of the interface pointers formerly available only to R.app are now
      available to front-ends on all Unix-alikes: one has been added
      for the interface to View().

PACKAGE = "" is now an error in .C() etc calls: it was always contrary
      to the documentation.

Entry point rcont2 has been migrated to package stats and so is no
      longer available.

R_SVN_REVISION in Rversion.h is now an integer (rather than a string)
      and hence usable as e.g.  #if R_SVN_REVISION < 70000.

The entry points rgb2hsv and hsv2rgb have been migrated to package
      grDevices and so are no longer available.

R_GE_version has been increased to 10 and name2col removed (use
      R_GE_str2col instead).  R internal colour codes are now defined
      using the typedef rcolor.

The REPROTECT macro now checks that the protect index is valid.

Several non-API entry points no longer used by R have been removed,
      including the Fortran entry points chol, chol2inv, cg, ch and rg,
      and the C entry points Brent_fmin, fft_factor and fft_work.

If a .External call is registered with a number of arguments (other
      than -1), the number of arguments passed is checked for each call
      (as for other foreign function calls).

It is now possible to write custom connection implementations outside
      core R using R_ext/Connections.h.  Please note that the
      implementation of connections is still considered internal and
      may change in the future (see the above file for details).

  INTERNATIONALIZATION:

The management of translations has been converted to R code: see
      ?tools::update_pkg_po.

The translations for the R interpreter and RGui.exe are now part of the
      base package (rather than having sources in directory po and
      being installed to share/locale).  Thus the base package supports
      three translation domains, R-base, R and RGui.

The compiled translations which ship with R are all installed to the
      new package translations for easier updating.  The first package
      of that name found on .libPaths() at the start of the R session
      will be used.  (It is possible messages will be used before
      .libPaths() is set up in which case the default translations will
      be used: set environment variable R_TRANSLATIONS to point to the
      location of the intended translations package to use this right
      from the start.)

The translations form a separate group in the Windows installer, so can
      be omitted if desired.

The markup for many messages has been changed to make them

  INSTALLATION:



make pdf and make install-pdf now make and install the full reference
      index (including all base and recommended packages).

The 'reference manual' on the Windows GUI menu and included in the
      installer is now the full reference index, including all base and
      recommended packages.

R help pages and manuals have no ISBNs because ISBN rules no longer
      allow constantly changing content to be assigned an ISBN.

The Windows installer no longer installs a Start Menu link to the
      static help pages; as most pages are generated dynamically, this
      led to a lot of broken links.

Any custom settings for Java configuration are recorded in file
      etc/javaconf for subsequent use by R CMD javareconf.

There is now support for makeinfo version 5.0 (which requires a
      slightly different .texi syntax).

The minimum versions for --use-system-zlib and --use-system-pcre are
      now tested as 1.2.5 and 8.10 respectively.

On Windows, the stack size is reduced to 16MB on 32-bit systems:
      misguided users were launching many threads without controlling
      the stack size.

configure no longer looks for file ~/.Rconfig: ~/.R/config has long
      been preferred.

  BUG FIXES:

When R CMD build is run in an encoding other than the one specified in
      the package's DESCRIPTION file it tries harder to expand the
      authors@R field in the specified encoding.  (PR#14958)

If R CMD INSTALL is required to expand the authors@R field of the
      DESCRIPTION file, it tries harder to do so in the encoding
      specified for the package (rather than using ASCII escapes).

Fix in package grid for pushing a viewport into a layout cell, where
      the layout is within a viewport that has zero physical width OR
      where the layout has zero total relative width (likewise for
      height).  The layout column widths (or row heights) in this case
      were being calculated with non-finite values.  (Reported by
      Winston Chang.)

solve(A, b) for a vector b gave the answer names from colnames(A) for
      LINPACK = TRUE but not in the default case.

La.svd() accepts logical matrices (as documented, and as svd() did).

legend() now accepts negative pch values, in the same way points() long
      has.

Parse errors when installing files now correctly display the name of
      the file containing the bad code.

In Windows, tcltk windows were not always properly constructed.
      (PR#15150)

The internal functions implementing parse(), tools::parseLatex() and
      tools::parse_Rd() were not reentrant, leading to errors in rare
      circumstances such as a garbage collection triggering a recursive
      call.

Field assignments in reference class objects via $<- were not being
      checked because the magic incantation to turn methods on for that
      primitive operator had been inadvertently omitted.

setHook(hookname, value, action="replace") set the hook to be the
      value, rather than a list containing the value as documented.
      (PR#15167)

 If a package used a NEWS.Rd file, the main HTML package index page did
      not link to it.  (Reported by Dirk Eddelbuettel.)

The primitive implementation of @<- was not checking the class of the
      replacement.  It now does a check, quicker but less general than
      slot<-. See the help.

split(x, f) now recycles classed objects x in the same way as vectors.
      (Reported by Martin Morgan.)

pbeta(.28, 1/2, 2200, lower.tail=FALSE, log.p=TRUE) is no longer -Inf;
      ditto for corresponding pt() and pf() calls, such as pt(45,
      df=5000, lower.tail=FALSE, log.p=TRUE). (PR#15162)

The Windows graphics device would crash R if a user attempted to load
      the graphics history from a variable that was not a saved
      history. (PR#15230)

The workspace size for the predict() method for loess() could exceed
      the maximum integer size.  (Reported by Hiroyuki Kawakatsu.)

ftable(x, row.vars, col.vars) now also works when the *.vars arguments
      are (integer or character vectors) of length zero.

Calling cat() on a malformed UTF-8 string could cause the Windows GUI
      to lock up. (PR#15227)

removeClass(cc) gave "node stack overflow" for some class definitions
      containing "array" or "matrix".

CHANGES in previous versions:

Older news can be found in text format in files NEWS.0, NEWS.1 and
    NEWS.2 in the doc directory.  News in HTML format for R versions
    from 2.10.0 to 2.15.3 is in doc/html/NEWS.2.html.

