[pkgsrc/trunk]: pkgsrc/math/R Update to 2.14.2

[markd <markd%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/3afcc87a6cc1
branches:  trunk
changeset: 602490:3afcc87a6cc1
user:      markd <markd%pkgsrc.org@localhost>
date:      Sun Apr 15 03:29:47 2012 +0000

description:
Update to 2.14.2

CHANGES IN R VERSION 2.14.2:

  NEW FEATURES:

    o The internal untar() (as used by default by R CMD INSTALL) now
      knows about some pax headers which bsdtar (e.g., the default tar
      for Mac OS >= 10.6) can incorrectly include in tar files, and
      will skip them with a warning.

    o Function compactPDF() in package tools now takes the default for
      argument gs_quality from environment variable GS_QUALITY: there
      is a new value "none", the ultimate default, which prevents
      GhostScript being used in preference to qpdf just because
      environment variable R_GSCMD is set.  If R_GSCMD is unset or set
      to "", the function will try to find a suitable GhostScript
      executable.

    o For consistency with the logLik() method, nobs() for "nls" files
      now excludes observations with zero weight.  (Reported by Berwin
       Turlach.)

  UTILITIES:

    o R CMD check now reports by default on licenses not according to
      the description in 'Writing R Extensions'.

    o R CMD check has a new option --as-cran to turn on most of the
      customizations that CRAN uses for its incoming checks.

  PACKAGE INSTALLATION:

    o R CMD INSTALL will now no longer install certain file types from
      inst/doc: these are almost certainly mistakes and for some
      packages are wasting a lot of space.

  + BUG FIXES

CHANGES IN R VERSION 2.14.1:

  NEW FEATURES:

    o parallel::detectCores() is now able to find the number of
      physical cores (rather than CPUs) on Sparc Solaris.

      It can also do so on most versions of Windows; however the
      default remains detectCores(logical = TRUE) on that platform.

    o Reference classes now keep a record of which fields are locked.
      $lock() with no arguments returns the names of the locked fields.

    o HoltWinters() reports a warning rather than an error for some
      optimization failures (where the answer might be a reasonable
      one).

    o tools::dependsOnPkg() now accepts the shorthand dependencies =
      "all".

    o parallel::clusterExport() now allows specification of an
      environment from which to export.

    o The quartz() device now does tilde expansion on its file
      argument.

    o Option print in Sweave's RweaveLatex() driver now emulates
      auto-printing rather than printing (which can differ for an S4
      object by calling show() rather than print()).

    o filled.contour() now accepts infinite values: previously it might
      have generated invalid graphics files (e.g. containing NaN
      values).

  + BUG FIXES

diffstat:

 math/R/Makefile                      |   5 ++---
 math/R/PLIST                         |  14 +++-----------
 math/R/distinfo                      |   9 ++++-----
 math/R/patches/patch-src_main_util.c |  26 --------------------------
 4 files changed, 9 insertions(+), 45 deletions(-)

diffs (118 lines):

diff -r 67eb3acea544 -r 3afcc87a6cc1 math/R/Makefile
--- a/math/R/Makefile   Sun Apr 15 03:05:02 2012 +0000
+++ b/math/R/Makefile   Sun Apr 15 03:29:47 2012 +0000
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.125 2012/03/03 00:13:32 wiz Exp $
+# $NetBSD: Makefile,v 1.126 2012/04/15 03:29:47 markd Exp $
 
-DISTNAME=              R-2.14.0
-PKGREVISION=           3
+DISTNAME=              R-2.14.2
 CATEGORIES=            math
 MASTER_SITES=          ${MASTER_SITE_R_CRAN:=base/R-2/}
 
diff -r 67eb3acea544 -r 3afcc87a6cc1 math/R/PLIST
--- a/math/R/PLIST      Sun Apr 15 03:05:02 2012 +0000
+++ b/math/R/PLIST      Sun Apr 15 03:29:47 2012 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.13 2011/12/11 18:41:47 markd Exp $
+@comment $NetBSD: PLIST,v 1.14 2012/04/15 03:29:48 markd Exp $
 bin/R
 bin/Rscript
 lib/R/COPYING
@@ -198,9 +198,6 @@
 lib/R/library/Matrix/doc/Comparisons.R
 lib/R/library/Matrix/doc/Comparisons.Rnw
 lib/R/library/Matrix/doc/Comparisons.pdf
-lib/R/library/Matrix/doc/DSC2009_abstract.pdf
-lib/R/library/Matrix/doc/DSC2009_abstract.tex
-lib/R/library/Matrix/doc/DSC2009_abstract.txt
 lib/R/library/Matrix/doc/Design-issues.R
 lib/R/library/Matrix/doc/Design-issues.Rnw
 lib/R/library/Matrix/doc/Design-issues.pdf
@@ -217,9 +214,7 @@
 lib/R/library/Matrix/doc/UFsparse/SPQR.txt
 lib/R/library/Matrix/doc/UFsparse/UFconfig.txt
 lib/R/library/Matrix/doc/UFsparse/UserGuides.txt
-lib/R/library/Matrix/doc/fullpage.sty
 lib/R/library/Matrix/doc/index.html
-lib/R/library/Matrix/doc/myVignette.sty
 lib/R/library/Matrix/doc/sparseModels.R
 lib/R/library/Matrix/doc/sparseModels.Rnw
 lib/R/library/Matrix/doc/sparseModels.pdf
@@ -1099,6 +1094,7 @@
 lib/R/library/stats4/po/ru/LC_MESSAGES/R-stats4.mo
 lib/R/library/stats4/po/tr/LC_MESSAGES/R-stats4.mo
 lib/R/library/stats4/po/zh_CN/LC_MESSAGES/R-stats4.mo
+lib/R/library/survival/CITATION
 lib/R/library/survival/DESCRIPTION
 lib/R/library/survival/INDEX
 lib/R/library/survival/Meta/Rd.rds
@@ -1116,14 +1112,11 @@
 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/doc/cgd.dat
-lib/R/library/survival/doc/d3.rda
 lib/R/library/survival/doc/index.html
-lib/R/library/survival/doc/raheart.rda
 lib/R/library/survival/doc/timedep.R
 lib/R/library/survival/doc/timedep.Rnw
 lib/R/library/survival/doc/timedep.pdf
-lib/R/library/survival/doc/validate.tex
+lib/R/library/survival/doc/validate.pdf
 lib/R/library/survival/help/AnIndex
 lib/R/library/survival/help/aliases.rds
 lib/R/library/survival/help/paths.rds
@@ -1320,4 +1313,3 @@
 lib/pkgconfig/libR.pc
 man/man1/R.1
 man/man1/Rscript.1
-@pkgdir lib/R/doc/manual
diff -r 67eb3acea544 -r 3afcc87a6cc1 math/R/distinfo
--- a/math/R/distinfo   Sun Apr 15 03:05:02 2012 +0000
+++ b/math/R/distinfo   Sun Apr 15 03:29:47 2012 +0000
@@ -1,9 +1,8 @@
-$NetBSD: distinfo,v 1.47 2012/03/06 21:34:29 wiz Exp $
+$NetBSD: distinfo,v 1.48 2012/04/15 03:29:48 markd Exp $
 
-SHA1 (R-2.14.0.tar.gz) = 0f46bf75a7c150350b1142c29a98e7994d2b4bef
-RMD160 (R-2.14.0.tar.gz) = f2f2805c8660d58050be1d11abf376843dbb40ea
-Size (R-2.14.0.tar.gz) = 22675106 bytes
+SHA1 (R-2.14.2.tar.gz) = 523dca7694e4d0c8701fcc783ea3767e46fe7a62
+RMD160 (R-2.14.2.tar.gz) = 6055dd28a99baa7b23c55f74dc1479e93a0dee58
+Size (R-2.14.2.tar.gz) = 23893986 bytes
 SHA1 (patch-ac) = ea885d8391ec06a7cc7fcbbadce134c794b7a47c
 SHA1 (patch-ad) = 43ae23bd0815986c3bac661bd3354cd96b3e54e4
 SHA1 (patch-src_main_format.c) = f337358361cd81547305d61be4682c4f73b6531a
-SHA1 (patch-src_main_util.c) = ef4d1bc426f49f51903cf2da66897cfa023b2092
diff -r 67eb3acea544 -r 3afcc87a6cc1 math/R/patches/patch-src_main_util.c
--- a/math/R/patches/patch-src_main_util.c      Sun Apr 15 03:05:02 2012 +0000
+++ /dev/null   Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-$NetBSD: patch-src_main_util.c,v 1.1 2012/03/06 21:34:29 wiz Exp $
-
-Fix build with pcre-8.30+.
-Based on Petr Písař <ppisar%redhat.com@localhost>'s patch
-http://pkgs.fedoraproject.org/gitweb/?p=R.git;a=commitdiff_plain
-
---- src/main/util.c.orig       2011-10-02 22:02:33.000000000 +0000
-+++ src/main/util.c
-@@ -1257,8 +1257,16 @@ Rboolean mbcsValid(const char *str)
- }
- 
- #include "pcre.h"
-+#if  PCRE_MAJOR > 8 || PCRE_MINOR >= 30
-+extern int _pcre_valid_utf(const char *string, int length, int *erroroffset);
-+
-+Rboolean utf8Valid(const char *str)
-+{
-+    int errp;
-+    return  (_pcre_valid_utf(str, (int) strlen(str), &errp) == 0);
-+}
- /* This changed at 8.13: we don't allow < 8.0 */
--#if  PCRE_MAJOR > 8 || PCRE_MINOR >= 13
-+#elif  PCRE_MAJOR > 8 || PCRE_MINOR >= 13
- extern int _pcre_valid_utf8(const char *string, int length, int *erroroffset);
- 
- Rboolean utf8Valid(const char *str)