R 2.10.1 is released

Peter Dalgaard P.Dalgaard at biostat.ku.dk
Mon Dec 14 11:20:20 CET 2009


R-2.10.1.tar.gz was built a short while ago.

This is a maintenance release and fixes a number of mostly minor issues.

See the full list of changes below.

You can get it from

http://cran.r-project.org/src/base/R-2/R-2.10.1.tar.gz

or wait for it to be mirrored at a CRAN site nearer to you. Binaries
for various platforms will appear in due course.


        For the R Core Team

        Peter Dalgaard


These are the md5sums for the freshly created files, in case you wish
to check that they are uncorrupted:

70447ae7f2c35233d3065b004aa4f331  INSTALL
433182754c05c2cf7a04ad0da474a1d0  README
4f004de59e24a52d0f500063b4603bcb  OONEWS
ff4bd9073ef440b1eb43b1428ce96872  ONEWS
08687cc1d9e5bb23875c1182f9f9cb2d  NEWS
d80a5c5808f038b36f79d8f0defaa0b9  THANKS
070cca21d9f8a6af15f992edb47a24d5  AUTHORS
a6f89e2100d9b6cdffcea4f398e37343  COPYING.LIB
eb723b61539feef013de476e68b5c50a  COPYING
020479f381d5f9038dcb18708997f5da  RESOURCES
4219bfcf875f995b84e5aebb1e02f3a5  FAQ
75f8b7e875b846ea96a4c6cc0abc00a4  R-2.10.1.tar.gz
75f8b7e875b846ea96a4c6cc0abc00a4  R-latest.tar.gz



Here is the relevant part of the NEWS file:

                CHANGES IN R VERSION 2.10.1

NEW FEATURES

    o   The PCRE library has been updated to version 8.00.

    o   R CMD INSTALL has new options --no-R, --no-libs, --no-data,
        --no-help, --no-demo, --no-exec, and --no-inst to suppress
        installation of the specified part of the package.  These are
        intended for special purposes (e.g. building a database
        of help pages without fully installing all packages).

    o   The documented line-length limit of 4095 bytes when reading
        from the console now also applies also to parse(file="")
        (which previously had a limit of around 1024 bytes).

    o   A Bioconductor mirror can be set for use by setRepositories()
        via the option "BioC_mirror", e.g. the European mirror can be
        selected by
        options(BioC_mirror="http://bioconductor.statistik.tu-dortmund.de")

    o   Double-clicking in a tk_select.list() list box now selects the
        item and closes the list box (as happens on the Windows
        select.list() widget).

INSTALLATION

    o   configure will be able to find a usable libtiff in some rare
        circumstances where it did not previously (where libtiff
        needed to be linked explicitly against -ljpeg).

    o   Making refman.pdf works around a problem with the indexing
        with hyperref 6.79d and later.

DEPRECATED & DEFUNCT

    o   The 'extended' argument is deprecated in strsplit(), grep(),
        grepl(), sub(), gsub(), regexpr() and gregexpr() (not just the
        value extended = FALSE) and will be removed in R 2.11.0.

BUG FIXES

    o   trigamma(x) and other psigamma(x, n) calls are now accurate for
        very large abs(x). (PR#14020)

    o   [g]sub(perl=FALSE, fixed=FALSE) could use excessive stack space
        when used with a very long vector containing some non-ASCII
        strings.

    o   The default method of weighted.mean(na.rm = TRUE) did not omit
        weights for NA observations in 2.10.0.  (PR#14032)

    o   [g]regexpr(pattern, fixed = TRUE) returned match positions in
        bytes (not characters) in an MBCS locale if 'pattern' was a
        single byte.

        [g]sub(fixed = TRUE) with a single-byte pattern could
        conceivably have matched part of a multibyte character in a
        non-UTF-8 MBCS.

    o   findLineNum() and setBreakpoint() would sometimes fail if the
        specified file was not in the current directory.

    o   Package tcltk's demo(tkdensity) was broken in 2.9.0 when demo()
        was changed to set par(ask = TRUE).

    o   gsub() with backrefs could fail on extremely long strings
        (hundreds of thousands of characters) due to integer overflow
        in a length calculation.

    o   abline(*, untf=TRUE) now uses a better x-grid in log-scale, e.g.,
        for plot(c(1,300), c(1,300), log="xy") ; abline(4,1, untf=TRUE).

    o   detach/unloadNamespace() arrange to flush the package's
        lazyload cache of R objects once the package/namespace is no
        longer needed.

    o   There have been small fixes to the rendering of help,
        e.g. \command is now rendered verbatim (so e.g. -- is not
        interpreted, PR#14045).

        Also, there are many small changes to help files where the new
        converters were not rendering them in the same way as before.

    o   available.packages() would fail when run on a repository
        with no packages meeting the filtering conditions. (PR#14042)

    o   rep(x, times, each = 2) gave invalid results when the 'times'
        argument is a vector longer than 'x'.  Reported by Bill Dunlap.

    o   An error when unloadNamespace() attempted to run the .onUnload()
        function gave an error in the reporting function and so was
        not reported properly.

    o   Text help rendering did not handle very long input lines
        properly.

    o   promptMethods() generated signature documentation improperly.

    o   pgamma(x, a, lower.tail=FALSE) and qgamma(..) are now
        considerably more accurate in some regions for very small 'a'.
        qgamma() now correctly returns 0 instead of NaN in similar
        extreme cases, and qgamma() no longer warns in the case of
        small 'a', see (PR#12324).

    o   unname() now also removes names from a zero length vector.

    o   Printing results from ls.str() no longer evaluates unevaluated
        calls.

    o   complete.cases() failed on a 0-column data frame argument.
        (Underlies PR#14066.)

        It could return nonsensical results if no input determined the
        number of cases (seen in the no-segfault tests).

    o   An error in nls() with a long formula could cause a segfault.
        (PR#14059)

    o   qchisq(p, df, ncp, lower.tail = FALSE) with ncp >= 80 was
        inaccurate for small p (as the help page said): it is now
        less inaccurate. (In part, PR#13999.)

        For ncp less than but close to 80, pchisq() and qchisq() are
        more accurate for probablilities very close to 1 (a series
        expansion was truncated slightly too early).

        pchisq(x, df, ncp) can no longer return values just larger
        than one for large values of ncp.

    o   intToUtf8() could fail when asked to produce 10Mb or more
        strings, something it was never intended to do: unfortunately
        Windows crashed R (other OSes reported a lack of resources).
        (PR#14068)

    o   chisq.test() could fail when given argument 'x' or 'y' which
        deparsed to more than one line.  (Reported by Laurent Gauthier.)

    o   S4 methods are uncached whenever the name space containing
        them is unloaded (by unloadNamespace() as well as by
        detach(unload = TRUE)).

    o   The internal record-keeping by dyn.load/dyn.unload was
        incomplete, which could crash R if a DLL that registered
        .External routines had earlier been unloaded.

    o   bessel[JY](x, nu) with nu a negative integer (a singular case)
        is now correct, analogously to besselI(), see PR#13556, below.

    o   tools::file_path_as_absolute() doubled the file separator when
        applied to a file such as "/vmunix" or (on Windows) "d:/afile"
        in a directory for which getwd() would return a path with a
        trailing separator (largely cosmetic, as reasonable file
        systems handle such a path correctly).  (Perhaps what was
        meant by PR#14078.)

    o   unsplit(drop = TRUE) applied to a data frame failed to pass
        'drop' to the computation of row names. (PR#14084)

    o   The "difftime" method of mean() ignored its 'na.rm' argument.

    o   tcltk::tk_select.list() is now more likely to remove the
        widget immediately after selection is complete.

    o   Adding/subtracting a "difftime" object to/from a "POSIXt" or
        "Date" object works again (it was broken by the addition of
        Ops.difftime).

    o   Conversion to latex of an Rd file with no aliases failed.

    o   wilcox.test(*, conf.int=TRUE) has achieved.level corrected and, for
        exact=FALSE, now gives an 'estimate' which does not depend on the
        alternative used.

    o   help.search() failed when the package argument was specified.
        (PR#14113)

    o   switch(EXPR = "A")  now returns NULL, as switch(1) {which used to
        signal an error}.



-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)              FAX: (+45) 35327907



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