Update to R 3.0.3. update from wen heping.

CHANGES IN R 3.0.3:

NEW FEATURES:

* On Windows there is support for making .texi manuals using
  texinfo 5.0 or later: the setting is in file
  src/gnuwin32/MkRules.dist.

  A packaging of the Perl script and modules for texinfo 5.2 has
  been made available at <URL:
  http://www.stats.ox.ac.uk/pub/Rtools/>.

* write.table() now handles matrices of 2^31 or more elements, for
  those with large amounts of patience and disc space.

* There is a new function, La_version(), to report the version of
  LAPACK in use.

* The HTML version of 'An Introduction to R' now has links to PNG
  versions of the figures.

* There is some support to produce manuals in ebook formats. (See
  doc/manual/Makefile.  Suggested by Mauro Cavalcanti.)

* On a Unix-alike Sys.timezone() returns NA if the environment
  variable TZ is unset, to distinguish it from an empty string
  which on some OSes means the UTC time zone.

* The backtick may now be escaped in strings, to allow names
  containing them to be constructed, e.g. `\``.

* read.table(), readLines() and scan() now warn when an embedded
  nul is found in the input.

* KalmanForecast(fast = FALSE) is now the default, and the help
  contains an example of how fast = TRUE can be used in this
  version.  (The usage will change in 3.1.0.)

* strptime() now checks the locale only when locale-specific
  formats are used and caches the locale in use: this can halve the
  time taken on OSes with slow system functions (e.g. OS X).

* strptime() and the format() methods for classes "POSIXct",
  "POSIXlt" and "Date" recognize strings with marked encodings:
  this allows, for example, UTF-8 French month names to be read on
  (French) Windows.

* iconv(to = "utf8") is now accepted on all platforms (some
  implementations did already, but GNU libiconv did not: however
  converted strings were not marked as being in UTF-8).  The
  official name, "UTF-8" is still preferred.

* available.packages() is better protected against corrupt metadata
  files.

* Finalizers are marked to be run at garbage collection, but run
  only at a somewhat safer later time (when interrupts are
  checked).  This circumvents some problems with finalizers running
  arbitrary code during garbage collection (the known instances
  being running options() and (C-level) path.expand()
  re-entrantly).

5 files changed, 0 insertions, 136 deletions

diff --git a/math/R/patches/patch-src_library_stats_src_cov.c b/math/R/patches/patch-src_library_stats_src_cov.c
deleted file mode 100644
index d2933585fc1..00000000000
--- a/math/R/patches/patch-src_library_stats_src_cov.c
+++ /dev/null
@@ -1,17 +0,0 @@
-$NetBSD: patch-src_library_stats_src_cov.c,v 1.1 2013/08/13 19:53:30 markd Exp $
-
-No sqrtl() in NetBSD 6.x
-
---- src/library/stats/src/cov.c.orig	2013-03-05 23:02:24.000000000 +0000
-+++ src/library/stats/src/cov.c
-@@ -27,6 +27,10 @@
- 
- #include "statsR.h"
- 
-+#ifdef __NetBSD__
-+#define sqrtl sqrt
-+#endif
-+
- static SEXP corcov(SEXP x, SEXP y, SEXP na_method, SEXP kendall, Rboolean cor);
- 
- 
diff --git a/math/R/patches/patch-src_main_format.c b/math/R/patches/patch-src_main_format.c
deleted file mode 100644
index 8d91689b1b3..00000000000
--- a/math/R/patches/patch-src_main_format.c
+++ /dev/null
@@ -1,71 +0,0 @@
-$NetBSD: patch-src_main_format.c,v 1.4 2013/08/13 19:53:30 markd Exp $
-
-NetBSD does not have rintl() or floorl() so use the OpenBSD implementation
-of rintl() in that case.  The same case exists for DragonFly.
-
---- src/main/format.c.orig	2013-03-05 23:02:40.000000000 +0000
-+++ src/main/format.c
-@@ -130,6 +130,7 @@ void formatInteger(int *x, R_xlen_t n, i
- # define R_nearbyintl rintl
- # else
- # define R_nearbyintl private_nearbyintl
-+# if !defined(__NetBSD__) && !defined(__DragonFly__)
- LDOUBLE private_nearbyintl(LDOUBLE x)
- {
-     LDOUBLE x1;
-@@ -142,6 +143,55 @@ LDOUBLE private_nearbyintl(LDOUBLE x)
-         if (x/2.0 == floorl(x/2.0)) return(x); else return(x1);
-     }
- }
-+# else
-+#include <machine/ieee.h>
-+
-+#if LDBL_MAX_EXP != 0x4000
-+/* We also require the usual bias, min exp and expsign packing. */
-+#error "Unsupported long double format"
-+#endif
-+
-+#define BIAS    (LDBL_MAX_EXP - 1)
-+
-+static const float
-+shift[2] = {
-+#if LDBL_MANT_DIG == 64
-+        0x1.0p63, -0x1.0p63
-+#elif LDBL_MANT_DIG == 113
-+        0x1.0p112, -0x1.0p112
-+#else
-+#error "Unsupported long double format"
-+#endif
-+};
-+static const float zero[2] = { 0.0, -0.0 };
-+
-+long double private_nearbyintl(long double x)
-+{
-+        union {
-+                long double e;
-+                struct ieee_ext bits;
-+        } u;
-+        uint32_t expsign;
-+        int ex, sign;
-+        u.e = x;
-+        expsign = (u.bits.ext_sign << 15) | u.bits.ext_exp;
-+        ex = expsign & 0x7fff;
-+
-+        if (ex >= BIAS + LDBL_MANT_DIG - 1) {
-+                if (ex == BIAS + LDBL_MAX_EXP)
-+                        return (x + x); /* Inf, NaN, or unsupported format */
-+                return (x);             /* finite and already an integer */
-+        }
-+        sign = expsign >> 15;
-+        x += shift[sign];
-+        x -= shift[sign];
-+
-+        if (ex < BIAS && x == 0.0L)
-+                return (zero[sign]);
-+
-+        return (x);
-+}
-+# endif
- # endif
- # else /* no long double */
- # ifdef HAVE_NEARBYINT
diff --git a/math/R/patches/patch-src_nmath_dnbeta.c b/math/R/patches/patch-src_nmath_dnbeta.c
deleted file mode 100644
index c66ef2d42f7..00000000000
--- a/math/R/patches/patch-src_nmath_dnbeta.c
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD: patch-src_nmath_dnbeta.c,v 1.2 2013/12/15 19:58:11 asau Exp $
-
-No logl() in NetBSD 6.x and FreeBSD 9.
-
---- src/nmath/dnbeta.c.orig	2013-03-05 23:02:41.000000000 +0000
-+++ src/nmath/dnbeta.c
-@@ -118,7 +118,7 @@ double dnbeta(double x, double a, double
- 	sum += term;
-     } while (term > sum * eps);
- 
--#ifdef HAVE_LONG_DOUBLE
-+#if defined(HAVE_LONG_DOUBLE) && ! defined(__NetBSD__) && ! defined(__FreeBSD__)
-     return R_D_exp((double)(p_k + logl(sum)));
- #else
-     return R_D_exp((double)(p_k + log(sum)));
diff --git a/math/R/patches/patch-src_nmath_pnbeta.c b/math/R/patches/patch-src_nmath_pnbeta.c
deleted file mode 100644
index 6284db756fb..00000000000
--- a/math/R/patches/patch-src_nmath_pnbeta.c
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD: patch-src_nmath_pnbeta.c,v 1.2 2013/12/15 19:58:11 asau Exp $
-
-No logl() in NetBSD 6.x and FreeBSD 9.
-
---- src/nmath/pnbeta.c.orig	2013-03-05 23:02:41.000000000 +0000
-+++ src/nmath/pnbeta.c
-@@ -92,7 +92,7 @@ pnbeta2(double x, double o_x, double a, 
- 
-     /* return R_DT_val(ans), but we want to warn about cancellation here */
-     if (lower_tail)
--#ifdef HAVE_LONG_DOUBLE
-+#if defined(HAVE_LONG_DOUBLE) && ! defined(__NetBSD__) && ! defined(__FreeBSD__)
- 	return (double) (log_p ? logl(ans) : ans);
- #else
- 	return log_p ? log(ans) : ans;
diff --git a/math/R/patches/patch-src_nmath_pnchisq.c b/math/R/patches/patch-src_nmath_pnchisq.c
deleted file mode 100644
index a579a77e37c..00000000000
--- a/math/R/patches/patch-src_nmath_pnchisq.c
+++ /dev/null
@@ -1,18 +0,0 @@
-$NetBSD: patch-src_nmath_pnchisq.c,v 1.2 2013/12/15 19:58:11 asau Exp $
-
-No expl() in NetBSD 6.x and FreeBSD 9.
-
---- src/nmath/pnchisq.c.orig	2013-03-05 23:02:41.000000000 +0000
-+++ src/nmath/pnchisq.c
-@@ -27,7 +27,11 @@
-  */
- 
- #ifdef HAVE_LONG_DOUBLE
-+#if defined(__NetBSD__) || defined(__FreeBSD__)
-+# define EXP exp
-+#else
- # define EXP expl
-+#endif
- # define FABS fabsl
- #else
- # define EXP exp