R 3.0.3 is released

March 10, 2014
By

(This article was first published on R-statistics blog » R, and kindly contributed to R-bloggers)

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 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
    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 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)

puuuuuuppy (image source)

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