R 3.0.3 is released

R 3.0.3 (codename “Warm Puppy) was released several days ago. The full list of new features and bug fixes is provided below.

Upgrading to R 3.0.3

You can download the latest version from here. Or, if you are using Windows, you can upgrade to the latest version using the installr package. Simply run the following code:

# installing/loading the package:
if(!require(installr)) { 
install.packages("installr"); require(installr)} #load / install+load installr
 
updateR()

I try to keep the installr package updated and useful. If you have any suggestions or remarks on the package, you’re invited to leave a comment below.

If you use the global library system (as I do), you can run the following in the new version of R:

source("http://www.r-statistics.com/wp-content/uploads/2010/04/upgrading-R-on-windows.r.txt")
New.R.RunMe()

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
  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.

• The HTML version of ‘An Introduction to R’ now has
  links to PNG versions of the figures.

• 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

• The included version of PCRE has been updated to 8.34. This
  fixes bugs and makes the behaviour closer to Perl 5.18. In
  particular, the concept of ‘space’ includes VT and
  hence agrees with POSIX’s.

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 < face="Courier New,Courier" color="#666666">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 < face="Courier New,Courier" color="#666666">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
  have been identified using the ‘Undefined Behaviour
  Sanitizer’ in conjunction with the clang compiler.

• 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.

• As a result of the 3.0.2 change about ‘the last
  second before the epoch’, most conversions which should have given
  NA returned that time. (The platforms affected include
  Linux and OS X, but not Windows nor Solaris.)

• 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 < face="Courier New,Courier" color="#666666">R< > code in a tcltk callback failed to set the
  busy flag, which will be needed to tell OS X not to ‘App Nap’.

• 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)