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PR/15396 CVS commit: pkgsrc/math/R

The following reply was made to PR pkg/15396; it has been noted by GNATS.

From: "Mark Davies" <>
Subject: PR/15396 CVS commit: pkgsrc/math/R
Date: Thu, 6 Feb 2014 10:57:21 +0000

 Module Name:   pkgsrc
 Committed By:  markd
 Date:          Thu Feb  6 10:57:21 UTC 2014
 Modified Files:
        pkgsrc/math/R: Makefile PLIST distinfo
 Removed Files:
        pkgsrc/math/R/patches: patch-doc_manual_R-defs.texi
 Log Message:
 Update to R 3.0.2
 * The NEWS files have been re-organized.
   This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y
   and 2.x.y releases is in files NEWS.0, NEWS.1 and NEWS.2.  The
   latter files are now installed when R is installed.  An HTML
   version of news from 2.10.0 to 2.15.3 is available as
 * sum() for integer arguments now uses an integer accumulator of at
   least 64 bits and so will be more accurate in the very rare case
   that a cumulative sum exceeds 2^53 (necessarily summing more than
   4 million elements).
 * The example() and tools::Rd2ex() functions now have parameters to
   allow them to ignore \dontrun markup in examples.  (Suggested by
   Peter Solymos.)
 * str(x) is considerably faster for very large lists, or factors
   with 100,000 levels, the latter as in PR#15337.
 * col2rgb() now converts factors to character strings not integer
   codes (suggested by Bryan Hanson).
 * tail(warnings()) now works, via the new `[` method.
 * There is now support for the LaTeX style file zi4.sty which has
   in some distributions replaced inconsolata.sty.
 * unlist(x) now typically returns all non-list xs unchanged, not
   just the "vector" ones.  Consequently, format(lst) now also works
   when the list lst has non-vector elements.
 * The tools::getVignetteInfo() function has been added to give
   information about installed vignettes.
 * New assertCondition(), etc. utilities in tools, useful for
 * Profiling now records non-inlined calls from byte-compiled code
   to BUILTIN functions.
 * Various functions in stats and elsewhere that use non-standard
   evaluation are now more careful to follow the namespace scoping
   rules.  E.g. stats::lm() can now find stats::model.frame() even
   if stats is not on the search path or if some package defines a
   function of that name.
 * If an invalid/corrupt .Random.seed object is encountered in the
   workspace it is ignored with a warning rather than giving an
   error.  (This allows R itself to rely on a working RNG, e.g. to
   choose a random port.)
 * seq() and give more explicit error messages if called
   with invalid (e.g. NaN) inputs.
 * When parse() finds a syntax error, it now makes partial parse
   information available up to the location of the error.  (Request
   of Reijo Sund.)
 * Methods invoked by NextMethod() had a different dynamic parent to
   the generic. This was causing trouble where S3 methods invoked
   via lazy evaluation could lose track of their generic.
 * Code for the negative binomial distribution now treats the case
   size == 0 as a one-point distribution at zero.
 * abbreviate() handles without warning non-ASCII input strings
   which require no abbreviation.
 * read.dcf() no longer has a limit of 8191 bytes per line. (Wish of
 * formatC(x) no longer copies the class of x to the result, to
   avoid misuse creating invalid objects as in PR#15303.  A warning
   is given if a class is discarded.
 * Dataset npk has been copied from MASS to allow more tests to be
   run without recommended packages being installed.
 * The initialization of the regression coefficients for
   non-degenerate differenced models in arima() has been changed and
   in some examples avoids a local maximum.  (PR#15396)
 * termplot() now has an argument transform.x to control the display
   of individual terms in the plot.  (PR#15329)
 * format() now supports digits = 0, to display nsmall decimal
 * There is a new read-only par() parameter called "page", which
   returns a logical value indicating whether the next
   call will start a new page.
 * Processing Sweave and Rd documents to PDF now renders backticks
 * utils::modifyList() gets a new argument keep.null allowing NULL
   components in the replacement to be retained, instead of causing
   corresponding components to be deleted.
 * tools::pkgVignettes() gains argument check; if set to TRUE, it
   will warn when it appears a vignette requests a non-existent
   vignette engine.
 To generate a diff of this commit:
 cvs rdiff -u -r1.143 -r1.144 pkgsrc/math/R/Makefile
 cvs rdiff -u -r1.17 -r1.18 pkgsrc/math/R/PLIST
 cvs rdiff -u -r1.56 -r1.57 pkgsrc/math/R/distinfo
 cvs rdiff -u -r1.1 -r0 pkgsrc/math/R/patches/patch-doc_manual_R-defs.texi \
 Please note that diffs are not public domain; they are subject to the
 copyright notices on the relevant files.

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