Update R to version 1.6.1.

Pkgsrc changes:
Now builds the libR.so and provides a buildlink2.mk for packages that want
to use it.  From suggestions from Kent Polk.

Recommended library set is now included in the base package.

Changes:
               CHANGES IN R VERSION 1.6.1

NEW FEATURES

    o   Added a few "trivial and obviously missing" functions to tcltk:
        tkchooseDirectory, tkpopup, tkdialog, tkread

    o   barplot() has a new argument `axis.lty', which if set to 1
        allows the pre-1.6.0 behaviour of plotting the axis and tick
        marks for the categorical axis.  (This was apparently not
        intentional, but axis() used to ignore lty=0.)
        The argument `border' is no longer ".NotYetUsed".


                CHANGES IN R VERSION 1.6.0

USER-VISIBLE CHANGES

    o   The default colour palette now has "grey" instead of "white"
        in location 8.  See palette().

    o   grid(nx) behaves differently (but the same as in R versions <= 0.64).

NEW FEATURES

    o   Preparations for name space support:

    o   The objects created in the methods package to represent
        classes, generic functions, method definitions, and
        inheritance relations now themselves belong to true classes.  In
        particular, the "classRepresentation" objects follow the description
        in "Programming with Data" (section 7.6).

    o   Other additions and changes to the methods package:

    o   New methods ([[, print, str) and extended plot() method
        (incl. logical `horiz') for "dendrogram" class.

    o   sprintf() now checks the agreement between formats and object
        types, and handles special values (NA, Inf, ...) correctly.

    o   chol() now uses a tolerance for non-positive-definiteness and
        so should give more consistent results across platforms.

    o   New function agrep() for approximate (fuzzy) string matching.

    o   help.search() can now use both approximate (fuzzy) and regular
        expression matching.  By default, if the pattern to be matched
        consists of only alphanumeric characters, whitespace or a dash,
        approximate matching is used.

    o   axis() has three new optional arguments `col', `lty', and `lwd'
        all for drawing the axis line and tick marks.

    o   Function vcov() (formerly in MASS), a generic function to
        return the variance-covariance matrix of the parameter
        estimates of a fitted model.

    o   duplicated() and unique() have methods for matrices and arrays
        (based on ideas from Jens Oehlschl<E4>gel).

    o   Internally memory sizes and counts of cons cells are now stored
        in unsigned longs.  This allows memory limits to be set and
        objects created in the range 2-4Gb on 32-bit platforms, and
        allows 64-bit platforms to use much larger amounts of memory.

    o   Command-line flags to set memory can now use the suffix `G'
        for gigabytes.  The setting of maximum vsize is now only
        limited by the platform's address space.

    o   All warning and error messages are truncated to a length set
        by options(warning.length=), defaulting to 1000.  (Previously
        most (but not quite all) were truncated at 8192 characters.)

    o   [dpqr]gamma() check for shape parameter > 0.

    o   as.POSIX[cl]t can now convert logical NAs.

    o   All installed packages (even those shipped with R) are
        given a `Built' field in the DESCRIPTION file.

    o   as.data.frame() now coerces logical matrices into logical
        columns (rather than factors).

    o   [[<-.data.frame no longer coerces character replacement values
        to factor.  This is consistent with using $ to replace and
        with S4.

    o   library() attempts to detect improperly installed packages, so
        as from this version an installed package must have a
        DESCRIPTION file and that file must have been stamped with a
        `Built:' line (which was introduced in 1.2.0).  Under
        Unix-alikes, the platform is checked against that used for
        installation.

    o   print.factor() has new arguments `max.levels' (with a smart default)
        and `width'.  print.ordered() is no longer needed.

    o   RNGkind() has an additional option for normal random generators:
        "Inversion".

    o   data.frame() recycles factors and "AsIs" objects as well as
        atomic vectors.

    o   rect() accepts additional graphics parameters through a ...
        argument (in the same way as polygon).

    o   strwidth/strheight() now coerce their first argument in exactly
        the same way text() does, so a wider range of inputs is allowed.

    o   prompt()'s default and data.frame methods have a new 3rd argument
        `name' allowing them to used more easily in scripts and loops.

    o   rgb() has a new `maxColorValue' argument, allowing r,g,b in [0,M],
        particularly in {0:255}, efficiently and non-error-prone.

    o   summaryRprof() provides the functionality of R CMD Rprof in R
        code, though more slowly.

    o   pdf() now uses PDF not R code for clipping, which ensures that
        partially visible text strings are (partially) shown.

    o   Each R session uses a per-session temporary directory which
        is removed at normal termination.  The directory name is given
        by the tempdir() function, and filenames returned by
        tempfile() will be within that directory.

   o   help.start() on Unix now uses a .R subdirectory of the
        per-session temporary directory and not ~/.R.  A side effect
        is that ~/.R is now never deleted by R.

    o   cbind/rbind() used to ignore all zero-length vectors, an
        undocumented quirk for S-compatibility.  This caused problems
        when combining zero-extent matrices and zero-length vectors, and
        now zero-length vectors are ignored unless the result would
        have zero rows/columns.

    o   plot.spec(x) now also works for other x than AR and Pgram results.

    o   New functions La.chol() and La.chol2inv() for Cholesky
        decomposition and inverse of positive definite matrices using
        Lapack.

    o   Changes to the tcltk package

    o   New function axTicks() returning tick mark locations like axis().

    o   grid() has a more sensible default behavior.  Tick axis alignment
        only happens when no numbers of grid cells are specified.  New
        arguments lwd and equilogs; nx/ny = NA for not drawing, see ?grid.

    o   installed.packages() has a new argument `priority'.

    o   termplot() uses factor levels rather than 1,2,3... for x-axis.

    o   The trace() function has been robustified and a new function
        tracingState() added to turn tracing temporarily on and off.

    o   New cophenetic() in "mva" as utility for hierarchical clustering.

    o   p.adjust() has two new methods, 'Hommel' and 'FDR', contributed
        by Gordon Smyth <smyth@wehi.edu.au>.

    o   stars() now has add and plot arguments.

and lots of bug fixes.

1 files changed, 20 insertions, 7 deletions

diff --git a/math/R/distinfo b/math/R/distinfo
index a911529eea5..9ccff9a060d 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,8 +1,21 @@
-$NetBSD: distinfo,v 1.10 2002/09/09 00:59:01 markd Exp $
+$NetBSD: distinfo,v 1.11 2002/12/10 11:58:10 markd Exp $
 
-SHA1 (R-1.5.1.tgz) = 3c0a09461ad49118935ed97fafb7076e690e59de
-Size (R-1.5.1.tgz) = 5452320 bytes
-SHA1 (patch-aa) = 6c2ad392e10ad51c7af717fd39f25b82ea2ed25c
-SHA1 (patch-ab) = 4704a191118a00bcddd09a0066322f35581653da
-SHA1 (patch-ac) = 4103e0197196fa96454e194c56bf169ccbc373d9
-SHA1 (patch-ad) = 92992b9485aeb6c132ea0e9fa80f66426cbfab83
+SHA1 (R-1.6.1.tgz) = 6f01abd81cb8ea28205e6511b0ecda826bcbaa84
+Size (R-1.6.1.tgz) = 8633830 bytes
+SHA1 (patch-aa) = 8ec7504d5c08e4258b0b1a433aed8760f630089e
+SHA1 (patch-ab) = a3bd4d27abbc7f26e223aaa1e559ccfc0e363c39
+SHA1 (patch-ac) = be0bb888da999cc571f048752204d478efa3d6ac
+SHA1 (patch-ad) = b9a08c37baaef8a7169208b758494a077ca531d6
+SHA1 (patch-ae) = 83f0f66d9b135eb81572e7f0be56c02bd95e44d1
+SHA1 (patch-af) = cf00c9bf60bf92aa27c33d750f55184c86be02f1
+SHA1 (patch-ag) = a4312c4f64ca0af1ee425ce25bef5fe06212e580
+SHA1 (patch-ah) = 37e2b7466ced465a412d1792fbcd17159f09aabf
+SHA1 (patch-ai) = 8a815753bbc2de4785b19ee3b3c2df4c9ca26578
+SHA1 (patch-aj) = 0a75114a5b34739f05418739c65e44e87ce024fb
+SHA1 (patch-ak) = 737a2329d14f5c6e516cf44cf66af421fc9a4b1c
+SHA1 (patch-al) = a2c582dd463bd85c6670ca981214c4a27bbdca5f
+SHA1 (patch-am) = 8ac2214f490f48f6cc780608b99cb07896a7fd7d
+SHA1 (patch-an) = dff4e97ca33fab0937c70b8dc3a8bcda799a4ab9
+SHA1 (patch-ao) = b94e2b6c8ad844be16f3dbcb9f96f7ba4f71094f
+SHA1 (patch-ap) = b2a273fe3865e8a7413762defb95966f54dd8de8
+SHA1 (patch-aq) = 36c7ad5c8ad0db9f9d879a196dfe9fb1dcc452d8