R-1.3.1 is released

[Peter Dalgaard BSA]

I've rolled up R-1.3.1.tgz a short while ago. This is a minor upgrade,
fixing a number of bugs and only containing a few small new features.
The most immediately visible new feature is that "less" is used for
viewing help pages if available.

A set of recommended packages which have been tested with R-1.3.1 has
been bundled up. Binary distributions are expected to include these
packages. The mgcv package is included this time (we intended to have
it in 1.3.0, but encountered portability problems).

Please note (as for 1.3.0) that the former "survival5" package is now
named "survival". If you install over an existing installation which
has survival5 installed, make sure to "R CMD REMOVE survival5"

You can get the files from the developer site

ftp://cvs.r-project.org/pub/CRAN/src/base/R-1.3.1.tgz
ftp://cvs.r-project.org/pub/CRAN/src/base/R-1.3.1-recommended.tgz

or

http://cvs.r-project.org/pub/CRAN/src/base/R-1.3.1.tgz
http://cvs.r-project.org/pub/CRAN/src/base/R-1.3.1-recommended.tgz

or wait for them to be mirrored at a CRAN site near you. This will
probably happen after the weekend due to circumstances in Vienna.
Binaries for various platforms will appear in due course.

There are also versions split for floppies, and a patch file relative
to R-1.3.0.


        For the R Core Team,

        Peter D.


Here's the relevant part of the NEWS file:


                CHANGES IN R VERSION 1.3.1


NEW FEATURES

    o   massage-examples is now a Perl script and about 50x faster.

    o   On Unix(-alike) systems the default pager is now determined
        during configuration, and is `less' if available, otherwise
        `more' (and not `more -s' as previously).

    o   configure now tests for strptime functions that fail on inputs
        before 1970 (found on Irix).  It no longer checks for the SCSL
        and SGIMATH libraries on Irix.

    o   New formula interface to cor.test() in package ctest.

    o   "NA" is now a valid color name (as NA has been a valid integer
        color).

    o   pairs() function has a new `gap' argument for adjusting the
        spacing between panels.

    o   R CMD check has a new test for unbalanced braces in Rd files.

    o   readBin() has a new argument `signed' to simplify reading
        unsigned 8- and 16-bit integers.

    o   New capabilities() option "cledit".

    o   Modified restore code to give clearer error messages in some cases.



BUG FIXES

    o   Fixed placement of mtext() output (including tick labels)
        when text is perpendicular to axis AND axis is logged
        (PR#997 and PR#865).

    o   rect() and arrows() now respond to setting of par(xpd)

    o   abline() now responds to the setting of par(xpd), including
        via the "..." argument (PR#750).

    o   Using cat() to a gzfile() connection no longer compresses poorly
        (at the expense of some latency).

    o   The `exact' p-values for the two-sided two-sample
        Kolmogorov-Smirnov test in 1.3.0 were for the wrong tail.

    o   In the HTML conversion of .Rd files, \link[foo]{bar} was
        ignoring [foo] outside \code{} statements.

    o   lm.influence(), plot.lm(), influence.measures() and the
        related diagnostic measures now handle lm() fits with
        na.action=na.exclude.

    o   Eliminated segmentation fault in while loops without braces
        in their bodies.

    o   barplot did not accept NA heights unless ylim was specified.

    o   predict.lm() failed with single-column model matrix (PR#1018).

    o   legend() now also works with 100s of entries (thanks to
        M. Schlather).

    o   A long-standing bug leading to inaccuracy in polyroot() has been
        fixed (PR#751)

    o   A very old bug with eval() not handling a numeric `envir' argument
        according to specifications has been fixed. [This in particular
        broke ported S-PLUS code that used eval(..., sys.parent())]. Also,
        eval() now checks that a numeric `envir' has length one to prevent
        accidental passing of matrices instead of data frames.

    o   The C code underlying nlm(f, *) now also works correctly when f(x)
        returns +Inf {nlm() itself *did* work!}.

    o   pdfcolor.tex is now included in doc/manual, as pdftex seems no
        longer to include it.

    o   Fixed protect bug in save() code that might have been responsible
        for occasionally saving corrupted workspaces.

    o   capabilities("X11") now reports if X11 is available in this
        session, thereby giving the correct answer if --gui=none was
        specified.

    o   Rd files with ,, inside \code{} were treating this as a
        ligature in LaTeX: now corrected in Rdconv.

    o   dlopen on Compaq Tru64 was finding the wrong entry points:
        worked-around by using different names in the modules.

    o   plot.mts() allows a type argument again (broken in 1.3.0: PR#1010).

    o   scan() has a limit of 8190 on the length of char strings, and
        now warns if it is exceeded (when the string has always been
        truncated).

    o   par adj now accepts values of integer mode (such as text(adj=0:1)).

    o   horizontal adj values outside the range [0, 1] are now
        supported on devices with canHAdj==1 (Windows devices, xfig).

    o   xtabs() without a response was ignoring drop.unused.levels=TRUE.

    o   readLines(ok=FALSE) was not generating an error when it should.

    o   princomp(covmat=) has been broken.

    o   Many documentation clean-ups: formerly undocumented arguments,
        use of T/F rather than TRUE/FALSE.

    o   df[] <- foo now works for data frames (PR#1047).

    o   nargs() was documented incorrectly.

    o   Using seq.POSIXt(by="2 weeks") was stepping by single weeks
        (PR#1046).

    o   dummy.coef.lm was not handling complex terms like z:I(x).
        It now either does or warns and gives NAs (PR#1048).

    o   predict.mlm() was broken (PR#1049).

    o   ksmooth (in package modreg) was using points to the left
        of the kernel under some circumstances (PR#1050).

    o   attr(x, "class") <- character(0) was segfaulting.  Similar problem
        with "comment" attribute also fixed.

    o   loadings() results from PCA (as well as from factor analysis)
        are now printed by print.loadings.

    o   Using chol() on an non-positive-definite matrix gave an
        misleading error message (PR#1061).

    o   as.character() on a language object was truncating to about 70
        characters: the internal limit (from the deparse code) is now the
        maximum possible 500.

    o   X11() device was failing to re-initialize correctly after all
        devices were shut down, so the colortype could not be changed
        and some systems showed protocol errors. (PR#1065)

    o   Converting Inf and NaN values by as.character() and reading by
        scan() was supported by strtod on some platforms and not
        others: these are now handled by R itself. (PR#1072)

    o   hclust(dist(1)) doesn't loop infinitely but signal an error.

    o   cutree() can now cut outside heights and does not return
        garbage for h >= max(tree$heights) anymore. (PR#1067)

    o   interaction(...,drop=F) returned an object looking like a
        factor, but with storage mode "double", confusing
        model.matrix.default (PR#1003)

    o   splineDesign(*, ord=) and others give better error messages for
        wrong `ord' (and have slightly improved documentation).



-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907
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