R 2.4.1 is released

[Peter Dalgaard]

I've rolled up R-2.4.1.tar.gz a short while ago. This is a maintenance
release and fixes a number of mostly minor bugs. See the full list
of changes below.

You can get it (in a short while) from

http://cran.r-project.org/src/base/R-2/R-2.4.1.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:

a8efde35b940278de19730d326f58449  AUTHORS
eb723b61539feef013de476e68b5c50a  COPYING
a6f89e2100d9b6cdffcea4f398e37343  COPYING.LIB
62b256c4a06aeed7401c9430f1e41d0f  FAQ
70447ae7f2c35233d3065b004aa4f331  INSTALL
06f14fbf950fbc7df31028344c78163b  NEWS
88bbd6781faedc788a1cbd434194480c  ONEWS
4f004de59e24a52d0f500063b4603bcb  OONEWS
92b33fd2c3e770d595c1a472889230d5  R-2.4.1.tar.gz
92b33fd2c3e770d595c1a472889230d5  R-latest.tar.gz
433182754c05c2cf7a04ad0da474a1d0  README
020479f381d5f9038dcb18708997f5da  RESOURCES
4eaf8a3e428694523edc16feb0140206  THANKS


Here is the relevant bit of the NEWS file:

               CHANGES IN R VERSION 2.4.1


INSTALLATION

    o   The extraction of info from Subversion for an SVN checkout now
        also works for svn >= 1.4.0.  However, on Windows the 'Last
        Changed Date' will be in the local timezone, and not in GMT as
        previously.

    o   configure uses code borrowed from autoconf 2.60 to try harder to
        ensure that a C99-compliant compiler is used.  (It does so by
        appending to CC.)  This avoids problems with systems such as FC5
        which override CFLAGS and thereby lose flags such as -std=gnu99.


NEW FEATURES

    o   rainbow(), heat.colors(), terrain.colors(), topo.colors() and
        cm.colors() all gain an 'alpha' argument to be passed to hsv().

    o   dput() will give an incorrect representation of the row names
        of a data frame with integer row names.  This is now corrected
        when the object is recreated.


C-LEVEL FACILITIES

    o   Using STRICT_R_HEADERS applies to more reported clashes with
        Windows headers, including Calloc and Realloc.  These and
        Free need to be prefixed by R_ when STRICT_R_HEADERS is defined.


DEPRECATED & DEFUNCT

    o   The previously undocumented behaviour of structure() in adding a
        class when specifying "tsp" or "levels" attributes is now
        deprecated (with a warning).


BUG FIXES

    o   Fixed warning() to use .dfltWarn intead of .dfltStop for default
        handling (PR#9274).

    o   R would slow down when the product of the length of a vector and
        the length of a character vector used to subset it exceeded 2^31.
        (PR#9280)

    o   merge() now allows zero-row data frames.

    o   add1.lm() had been broken by other changes for weighted fits.

    o   axis.POSIXct() would sometimes give the wrong labels.

    o   Help for a method call would fail. (PR#9291)

    o   gzfile() returned an object of class "file" not "gzfile". (PR#9271)

    o   load()ing from a connection had a logic bug in when it closed
        the connection. (PR#9271)

    o   The lowess() algorithm is unstable if the MAD of the residuals
        becomes (effectively) zero: R now terminates the iterations at
        that point.  (This may result in quite different answers.)

        The 'delta' argument was incorrectly documented.  (PR#9264)

    o   abbreviate() would only work for strings of up to 8191 bytes,
        but this was not checked.  Now longer strings are errors.

    o   Drawing X11 rotated text was buggy for VERY small (negative)
        angle of rotation.  Reported by Ben Bolker. (PR#9301)

    o   The X11 data editor would crash in an MBCS locale if R was
        compiled with FC's CFLAGS that add buffer overflow and
        stack-smashing detection.

    o   rect() was not accepting border=NA in some cases involving
        cross-hatching.

    o   Fixes to S4 group generics to ensure that the correct number of
        active arguments are in the signature of the group and all
        members.  Also a fix to keep the 'groupMembers' slot up to date.

    o   S4 group generic "Logic" (with '&', '|', but not '!') has been
        created, following the green book (apart from '!').

    o   removeClass() now takes care to remove any subclass references
        to the deleted class.

    o   mle() (in stats4) might not have worked as intended when the
        order of parameters in 'start' differed from that in the
        log-likelihood.  (PR#9313)

    o   dotchart() now properly restores par() settings after itself.

    o   system() on Mac OS X was blocking arbitrary signals during the
        call although only SIGPROF was meant to be blocked.

    o   methods cached via callNextMethod() and (sometimes) as() were
        being cached as directly specified although in fact they were
        inherited.  Caused problems in later search for inherited methods.

    o   str() works properly for method definitions and other S4-classed
        function objects.

    o   JAVA_LIBS are now set correctly on MacOS X.

    o   Fix null-termination issue suspected of causing crash with Fedora
        Extra RPMS (PR#9339, Justin Harrington, analysis and fix from Bill
        Dunlap).

    o   Namespaces restored via a saved session silently failed to cache
        their methods because the methods package was not yet
        attached.  Fixed by attaching methods before restoring data.

    o   rbind()ing a list to a data frame generated invalid row names,
        which were an error in 2.4.0. (PR#9346)

    o   boxplot.stats(x) now returns the correct minimum instead of an
        error for x <- c(1,Inf,Inf,Inf), and hence boxplot(x) "works".

    o   promptClass() now uses \linkS4class{<ClassName>} instead of
        of \link{<ClassName>-class}.

    o   gc() no longer reports nonsense values for the number of used
        Vcells if the true value exceeds 2^31 (and hence over 16Gb of
        heap is in use): it now reports NA. (PR#9345)

    o   rapply() now detects more user errors in supplying arguments.
(PR#9349)

    o   boxplot() was ignoring argument 'boxfill'. (PR#9352)

    o   plot.lm(which = 6, id.n = 0) did not work. (PR#9333)

    o   .deparseOpts("delayPromises") was not matching the C code,
        returning 64 rather than 32.

    o   bxp() could use partial matching on 'pars' when finding
        defaults for some of its parameters, e.g. a setting of 'cex.axis'
        in 'pars' or inline was used to set a default for 'outcex'.

    o   acf() now allows lag.max = 0 except when type="partial", and
        forces the lag 0 autocorrelation to 1. (PR#9360)

    o   hist(*, include.lowest=., right=., plot=FALSE) does not warn
        anymore, (PR#9356) and more.

    o   Some bugs in caching superclass/subclass relations and in
        removing those relations on detach and on removeClass() have
        been fixed.

    o   readBin() could return one too many strings if 'n' was an
        over-estimate. (PR#9361)

    o   A request for an opaque colour in the pdf() device after a
        translucent one did not set the transparency back to opaque in
        2.4.0.

        Semi-transparent background colours were not being plotted on
        the pdf() device.

    o   plot.lm(which=5) in the case of constant leverage re-ordered
        the factor levels but not the residuals, so the labelling by
        factor level was often incorrect.

    o   packBits() was not accepting a logical argument. (PR#9374)

    o   make install was omitting doc/FAQ and doc/RESOURCES.

    o   A two-sample t.test(x, y, var.equal=TRUE) did not allow one of the
        groups to be of size one.

    o   The "ts" method for print() failed on some corrupted objects
        of class "ts", e.g. those without a "tsp" attribute.

    o   structure() reordered the "class" value given if there was a
        "tsp" value specified.

    o   pairs() now does pass appropriate parts of '...' to the
        'diag.panel' argument. (PR#9384)

    o   plot.lm() was using an incorrect estimate of dispersion for
        some GLMs (including family=binomial and family=poisson).
        (PR#9316)

    o   Subsetting operators were setting R_Visible too early, so
        assignments in arguments could make the result invisible.
        (PR#9263)

    o   The tk-GUI was displaying a warning due to an extra comma in
        the list of manuals (PR#9396)

    o   packageDescription() now gives an explicit error on a corrupt
        DESCRIPTION file.

    o   There was a scoping issue with tcltk callbacks given as
        unevaluated expressions. This has only been partially fixed, a
        complete fix probably requires redesign.

    o   trace() had its return value documented incorrectly and was
        sometimes visible when it should not have been.

    o   pchisq() would sometimes use the wrong tail when calculating
        non-central probabilities with lower.tail = FALSE. (PR#9406)

    o   rm() could remove the wrong objects when passed an expression.
        (PR#9399)  Now only names are allowed in the '...' argument,
        and the incorrect documentation of what happened with
        character objects is corrected.

    o   url() was not supporting 'encoding' except on file:// URLs.



-- 
   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