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).

8 files changed, 28 insertions, 148 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index f09161e031e..ef36260eed5 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.146 2014/03/13 11:08:51 jperkin Exp $
+# $NetBSD: Makefile,v 1.147 2014/03/14 20:15:38 markd Exp $
 
-DISTNAME=		R-3.0.2
+DISTNAME=		R-3.0.3
 CATEGORIES=		math
 MASTER_SITES=		${MASTER_SITE_R_CRAN:=base/R-3/}
 
@@ -43,6 +43,11 @@ CONFIGURE_ARGS+=	--with-system-bzlib
 CONFIGURE_ARGS+=	--with-system-pcre
 CONFIGURE_ARGS+=	--with-system-xz
 
+.include "../../mk/bsd.prefs.mk"
+.if ${OPSYS} == "NetBSD" || ${OPSYS} == "FreeBSD"
+CONFIGURE_ARGS+=	--enable-long-double=no
+.endif
+
 # Disable Mac OS specific support used by R.app
 CONFIGURE_ARGS+=	--disable-R-framework
 CONFIGURE_ARGS+=	--without-aqua
diff --git a/math/R/PLIST b/math/R/PLIST
index fc1e7f13ba0..234978b0f96 100644
--- a/math/R/PLIST
+++ b/math/R/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.18 2014/02/06 10:57:21 markd Exp $
+@comment $NetBSD: PLIST,v 1.19 2014/03/14 20:15:38 markd Exp $
 bin/R
 bin/Rscript
 info/R-FAQ.info.gz
@@ -8,6 +8,12 @@ info/R-exts.info.gz
 info/R-intro.info.gz
 info/R-ints.info.gz
 info/R-lang.info.gz
+lib/R/doc/manual/images/QQ.png
+lib/R/doc/manual/images/ecdf.png
+lib/R/doc/manual/images/fig11.png
+lib/R/doc/manual/images/fig12.png
+lib/R/doc/manual/images/hist.png
+lib/R/doc/manual/images/ice.png
 lib/R/COPYING
 lib/R/NEWS
 lib/R/NEWS.0
@@ -236,6 +242,7 @@ lib/R/library/Matrix/external/USCounties_slots.rda
 lib/R/library/Matrix/external/lund_a.mtx
 lib/R/library/Matrix/external/lund_a.rsa
 lib/R/library/Matrix/external/pores_1.mtx
+lib/R/library/Matrix/external/symA.rda
 lib/R/library/Matrix/external/symW.rda
 lib/R/library/Matrix/external/test3comp.rda
 lib/R/library/Matrix/external/utm300.rua
@@ -976,6 +983,7 @@ lib/R/library/stats4/help/stats4.rdx
 lib/R/library/stats4/html/00Index.html
 lib/R/library/stats4/html/R.css
 lib/R/library/survival/CITATION
+lib/R/library/survival/COPYRIGHTS
 lib/R/library/survival/DESCRIPTION
 lib/R/library/survival/INDEX
 lib/R/library/survival/Meta/Rd.rds
@@ -993,7 +1001,15 @@ lib/R/library/survival/R/survival.rdx
 lib/R/library/survival/data/Rdata.rdb
 lib/R/library/survival/data/Rdata.rds
 lib/R/library/survival/data/Rdata.rdx
+lib/R/library/survival/data/datalist
+lib/R/library/survival/doc/adjcurve.R
+lib/R/library/survival/doc/adjcurve.Rnw
+lib/R/library/survival/doc/adjcurve.pdf
 lib/R/library/survival/doc/index.html
+lib/R/library/survival/doc/sourcecode.pdf
+lib/R/library/survival/doc/tests.R
+lib/R/library/survival/doc/tests.Rnw
+lib/R/library/survival/doc/tests.pdf
 lib/R/library/survival/doc/timedep.R
 lib/R/library/survival/doc/timedep.Rnw
 lib/R/library/survival/doc/timedep.pdf
diff --git a/math/R/distinfo b/math/R/distinfo
index 6e539ae3b0f..445776b3ef1 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,12 +1,7 @@
-$NetBSD: distinfo,v 1.57 2014/02/06 10:57:21 markd Exp $
+$NetBSD: distinfo,v 1.58 2014/03/14 20:15:38 markd Exp $
 
-SHA1 (R-3.0.2.tar.gz) = f5d9daef00e09d36a465ff7b0bf4cab136bea227
-RMD160 (R-3.0.2.tar.gz) = 8e91603754c965b402bb201c4e5f5a2043262537
-Size (R-3.0.2.tar.gz) = 25364181 bytes
+SHA1 (R-3.0.3.tar.gz) = 82e83415d27a2fbbdcacb41c4aa14d8b36fdf470
+RMD160 (R-3.0.3.tar.gz) = 9a7378732d3bc705092078e95e9c51d25c4be417
+Size (R-3.0.3.tar.gz) = 28075821 bytes
 SHA1 (patch-ac) = cbfe9853a6b1bdfa68d21c0a291f39545b131333
 SHA1 (patch-ad) = 21c2f74ceb41afa72b0b268ba4b1dcb57f01e106
-SHA1 (patch-src_library_stats_src_cov.c) = 23e452472506483ffc33a9c6629274b121cfd161
-SHA1 (patch-src_main_format.c) = f03012b8fbab34ead3f35143fe782ab7c7b29768
-SHA1 (patch-src_nmath_dnbeta.c) = 4711d17404352c9c190ca037a01b1eec1236cebc
-SHA1 (patch-src_nmath_pnbeta.c) = cb2de10d62abac32d6a1f40cdbb4de95c0462eed
-SHA1 (patch-src_nmath_pnchisq.c) = 312a2c726f98a8f4d6356b459086f20c55de5f1f
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