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
  doc/html/NEWS.2.html.

* 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
  testing.

* 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 seq.int() 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.
  (PR#15267)

* 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
  PR#15250.)

* 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
  places.

* There is a new read-only par() parameter called "page", which
  returns a logical value indicating whether the next plot.new()
  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.

2 files changed, 0 insertions, 79 deletions

diff --git a/math/R/patches/patch-doc_manual_R-defs.texi b/math/R/patches/patch-doc_manual_R-defs.texi
deleted file mode 100644
index 07670270e07..00000000000
--- a/math/R/patches/patch-doc_manual_R-defs.texi
+++ /dev/null
@@ -1,26 +0,0 @@
-$NetBSD: patch-doc_manual_R-defs.texi,v 1.1 2013/08/19 13:30:30 jperkin Exp $
-
-Texinfo 5.1 fixes.
-
---- doc/manual/R-defs.texi.orig	2013-04-03 22:05:07.000000000 +0000
-+++ doc/manual/R-defs.texi
-@@ -17,16 +17,17 @@ S
- @acronym{HTML}
- @end macro
- 
--@macro eqn {t, a}
- @iftex
-+@macro eqn {t, a}
- @tex
- $\t\$%
- @end tex
- @end iftex
- @ifnottex
-+@macro eqn {t, a}
- \a\@c
--@end ifnottex
- @end macro
-+@end ifnottex
- 
- @macro pkg {p}
- @strong{\p\}
diff --git a/math/R/patches/patch-doc_manual_R-intro.texi b/math/R/patches/patch-doc_manual_R-intro.texi
deleted file mode 100644
index 90a75e74cf0..00000000000
--- a/math/R/patches/patch-doc_manual_R-intro.texi
+++ /dev/null
@@ -1,53 +0,0 @@
-$NetBSD: patch-doc_manual_R-intro.texi,v 1.1 2013/08/19 13:30:30 jperkin Exp $
-
-Texinfo 5.1 fixes.
-
---- doc/manual/R-intro.texi.orig	2013-04-03 22:05:07.000000000 +0000
-+++ doc/manual/R-intro.texi
-@@ -1981,12 +1981,27 @@ is available, so we could have used @cod
- @node Matrix facilities, Forming partitioned matrices, Generalized transpose of an array, Arrays and matrices
- @section Matrix facilities
- 
-+@iftex
- @macro xTx{}
-- @eqn{@strong{x}^T @strong{x}, x'x}
-+@tex
-+@strong{x}^T @strong{x}$%
-+@end tex
- @end macro
- @macro xxT{}
-- @eqn{@strong{x}@strong{x}^T, x x'}
-+@tex
-+@strong{x}@strong{x}^T$%
-+@endtex
- @end macro
-+@end iftex
-+
-+@ifnottex
-+@macro xTx{}
-+x'x
-+@end macro
-+@macro xxT{}
-+x x'
-+@end macro
-+@end ifnottex
- 
- As noted above, a matrix is just an array with two subscripts.  However
- it is such an important special case it needs a separate discussion.
-@@ -2106,10 +2121,12 @@ potentially unstable to compute @code{x
- The quadratic form @eqn{@strong{x^T  A^{-1} x},@ @code{x %*% A^@{-1@} %*%
- x} @ } which is used in multivariate computations, should be computed by
- something like@footnote{Even better would be to form a matrix square
--root @eqn{B, B} with @eqn{A = BB^T, A = BB'} and find the squared length of the
--solution of @eqn{By = x, By = x}, perhaps using the Cholesky or
--eigendecomposition of @eqn{A, A}.} @code{x %*% solve(A,x)}, rather than
--computing the inverse of @code{A}.
-+root @eqn{B, B}
-+ with @eqn{A = BB^T, A = BB'}
-+ and find the squared length of the solution of
-+@eqn{By = x, By = x}
-+, perhaps using the Cholesky or eigendecomposition of @eqn{A, A}.
-+} @code{x %*% solve(A,x)}, rather than computing the inverse of @code{A}.
- 
- @node Eigenvalues and eigenvectors, Singular value decomposition and determinants, Linear equations and inversion, Matrix facilities
- @subsection Eigenvalues and eigenvectors