Update to R 3.1.0

 NEW FEATURES:

    * type.convert() (and hence by default read.table()) returns a
      character vector or factor when representing a numeric input as a
      double would lose accuracy.  Similarly for complex inputs.

      If a file contains numeric data with unrepresentable numbers of
      decimal places that are intended to be read as numeric, specify
      colClasses in read.table() to be "numeric".

    * tools::Rdiff(useDiff = FALSE) is closer to the POSIX definition
      of diff -b (as distinct from the description in the man pages of
      most systems).

    * New function anyNA(), a version of any(is.na(.)) which is fast
      for atomic vectors, based on a proposal by Tim Hesterberg.

    * arrayInd(*, useNames = TRUE) and, analogously, which(*, arr.ind =
      TRUE) now make use of names(.dimnames) when available.

    * is.unsorted() now also works for raw vectors.

    * The "table" method for as.data.frame() (also useful as
      as.data.frame.table()) now passes sep and base arguments to
      provideDimnames().

    * uniroot() gets new optional arguments, notably extendInt,
      allowing to auto-extend the search interval when needed.  The
      return value has an extra component, init.it.

    * switch(f, ...) now warns when f is a factor, as this typically
      happens accidentally where the useR meant to pass a character
      string, but f is treated as integer (as always documented).

    * The parser has been modified to use less memory.

    * The way the unary operators (+ - !) handle attributes is now more
      consistent.  If there is no coercion, all attributes (including
      class) are copied from the input to the result: otherwise only
      names, dims and dimnames are.

    * colorRamp() and colorRampPalette() now allow non-opaque colours
     and a ramp in opacity via the new argument alpha = TRUE.
      (Suggested by Alberto Krone-Martins, but optionally as there are
      existing uses which expect only RGB values.)

    * grid.show.layout() and grid.show.viewport() get an optional vp.ex
      argument.

    * There is a new function find_gs_cmd() in the tools package to
      locate a GhostScript executable.  (This is an enhanced version of
      a previously internal function there.)

    * object.size() gains a format() method.

    * There is a new family, "ArialMT", for the pdf() and postscript()
      devices.  This will only be rendered correctly on viewers which
      have access to Monotype TrueType fonts (which are sometimes
      requested by journals).

    * The text and PDF news files, including NEWS and NEWS.2, have been
      moved to the doc directory.

    * combn(x, simplify = TRUE) now gives a factor result for factor
      input x (previously user error).

    * Added utils::fileSnapshot() and utils::changedFiles() functions
      to allow snapshots and comparison of directories of files.

    * make.names(names, unique=TRUE) now tries to preserve existing
      names.

    * New functions cospi(x), sinpi(x), and tanpi(x), for more accurate
      computation of cos(pi*x), etc, both in R and the C API.  Using
      these gains accuracy in some cases, e.g., inside lgamma() or
      besselI().

    * print.table(x, zero.print = ".") now also has an effect when x is
      not integer-valued.

    * There is more support to explore the system's idea of time-zone
      names.  Sys.timezone() tries to give the current system setting
      by name (and succeeds at least on Linux, OS X, Solaris and
     Windows), and OlsonNames() lists the names in the system's Olson
      database. Sys.timezone(location = FALSE) gives the previous
      behaviour.

    * Platforms with a 64-bit time_t type are allowed to handle
      conversions between the "POSIXct" and "POSIXlt" classes for
      date-times outside the 32-bit range (before 1902 or after 2037):
      the existing workarounds are used on other platforms.  (Note that
      time-zone information for post-2037 is speculative at best, and
      the OS services are tested for known errors and so not used on OS
      X.)

      Currently time_t is usually long and hence 64-bit on Unix-alike
      64-bit platforms: however it several cases the time-zone database
      is 32-bit.  On R for Windows it is 64-bit (for both architectures
      as from this version).

    * The "save.defaults" option can include a value for
      compression_level.

    * colSums() and friends now have support for arrays and data-frame
      columns with 2^31 or more elements.

    * as.factor() is faster when f is an unclassed integer vector (for
      example, when called from tapply()).

    * fft() now works with longer inputs, from the 12 million
      previously supported up to 2 billion.

    * Complex svd() now uses LAPACK subroutine ZGESDD, the complex
      analogue of the routine used for the real case.

    * Sweave now outputs .tex files in UTF-8 if the input encoding is
      declared to be UTF-8, regardless of the local encoding.  The
      UTF-8 encoding may now be declared using a LaTeX comment
      containing the string %\SweaveUTF8 on a line by itself.

    * file.copy() gains a copy.date argument.

    * Printing of date-times will make use of the time-zone
      abbreviation in use at the time, if known.  For example, for
      Paris pre-1940 this could be LMT, PMT, WET or WEST.  To enable
      this, the "POSIXlt" class has an optional component "zone"
      recording the abbreviation for each element.

      For platforms which support it, there is also a component
      "gmtoff" recording the offset from GMT where known.

    * (On Windows, by default on OS X and optionally elsewhere.)  The
      system C function strftime has been replaced by a more
      comprehensive version with closer conformance to the POSIX 2008
      standard.

    * dnorm(x, log = FALSE) is more accurate (but somewhat slower) for
      |x| > 5.

    * Some versions of the tiff() device have further compression
      options.

    * read.table(), readLines() and scan() have a new argument to
      influence the treatment of embedded nuls.

    * Avoid duplicating the right hand side values in complex
      assignments when possible.  This reduces copying of replacement
      values in expressions such as Z$a <- a0 and ans[[i]] <- tmp: some
      package code has relied on there being copies.

      Also, a number of other changes to reduce copying of objects; all
      contributed by or based on suggestions by Michael Lawrence.

    * The fast argument of KalmanLike(), KalmanRun() and
      KalmanForecast() has been replaced by update, which instead of
      updating mod in place, optionally returns the updated model in an
      attribute "mod" of the return value.

    * arima() and makeARIMA() get a new optional argument SSinit,
      allowing the choice of a different *s*tate *s*pace initialization
      which has been observed to be more reliable close to
      non-stationarity.

    * warning() has a new argument noBreaks., to simplify
      post-processing of output with options(warn = 1).

    * pushBack() gains an argument encoding, to support reading of
      UTF-8 characters using scan(), read.table() and related functions
      in a non-UTF-8 locale.

    * all.equal.list() gets a new argument use.names which by default
      labels differing components by names (if they match) rather than
      by integer index.  Saved R output in packages may need to be
      updated.

    * The methods for all.equal() and attr.all.equal() now have
      argument check.attributes after ... so it cannot be partially nor
      positionally matched (as it has been, unintentionally).

      A side effect is that some previously undetected errors of
      passing empty arguments (no object between commas) to all.equal()
      are detected and reported.

      There are explicit checks that check.attributes is logical,
      tolerance is numeric and scale is NULL or numeric.  This catches
      some unintended positional matching.

      The message for all.equal.numeric() reports a "scaled difference"
      only for scale != 1.

    * all.equal() now has a "POSIXt" method replacing the "POSIXct"
      method.

    * The "Date" and "POSIXt" methods of seq() allows by = "quarter"
      for completeness (by = "3 months" always worked).

    * file.path() removes any trailing separator on Windows, where they
      are invalid (although sometimes accepted).  This is intended to
      enhance the portability of code written by those using POSIX file
      systems (where a trailing / can be used to confine path matching
      to directories).

    * New function agrepl() which like grepl() returns a logical
      vector.

    * fifo() is now supported on Windows.

    * sort.list(method = "radix") now allows negative integers

    * Some functionality of print.ts() is now available in
      .preformat.ts() for more modularity.

    * mcparallel() gains an option detach = TRUE which allows execution
      of code independently of the current session.  It is based on a
      new estranged = TRUE argument to mcfork() which forks child
      processes such that they become independent of the parent
      process.

    * The pdf() device omits circles and text at extremely small sizes,
      since some viewers were failing on such files.

    * The rightmost break for the "months", "quarters" and "years"
      cases of hist.POSIXlt() has been increased by a day.

    * The handling of DF[i,] <- a where i is of length 0 is improved.

    * hclust() gains a new method "ward.D2" which implements Ward's
      method correctly.  The previous "ward" method is "ward.D" now,
      with the old name still working.  Thanks to research and
      proposals by Pierre Legendre.

    * The sunspot.month dataset has been amended and updated from the
      official source, whereas the sunspots and sunspot.year datasets
      will remain immutable. The documentation and source links have
      been updated correspondingly.

    * The summary() method for "lm" fits warns if the fit is
      essentially perfect, as most of the summary may be computed
      inaccurately (and with platform-dependent values).

      Programmers who use summary() in order to extract just a
      component which will be reliable (e.g. $cov.unscaled) should wrap
      their calls in suppressWarnings().

4 files changed, 41 insertions, 25 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index ef36260eed5..4a8a7636223 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.147 2014/03/14 20:15:38 markd Exp $
+# $NetBSD: Makefile,v 1.148 2014/05/03 22:29:42 markd Exp $
 
-DISTNAME=		R-3.0.3
+DISTNAME=		R-3.1.0
 CATEGORIES=		math
 MASTER_SITES=		${MASTER_SITE_R_CRAN:=base/R-3/}
 
@@ -22,7 +22,6 @@ INSTALL_TARGET=		install install-info
 TEST_TARGET=		check
 USE_TOOLS+=		gmake gzip:run makeinfo perl:run sed unzip:run xmkmf
 USE_TOOLS+=		pkg-config
-USE_GNU_ICONV=		yes		# latin1 support, iconvlist
 USE_LANGUAGES=		c c++ fortran
 USE_LIBTOOL=		yes
 TEXINFO_REQD=		4.7
@@ -48,6 +47,10 @@ CONFIGURE_ARGS+=	--with-system-xz
 CONFIGURE_ARGS+=	--enable-long-double=no
 .endif
 
+.if ${OPSYS} != "Linux"
+USE_GNU_ICONV=		yes		# latin1 support, iconvlist
+.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 234978b0f96..daaf5d8c09c 100644
--- a/math/R/PLIST
+++ b/math/R/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.19 2014/03/14 20:15:38 markd Exp $
+@comment $NetBSD: PLIST,v 1.20 2014/05/03 22:29:42 markd Exp $
 bin/R
 bin/Rscript
 info/R-FAQ.info.gz
@@ -8,18 +8,7 @@ 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
-lib/R/NEWS.1
-lib/R/NEWS.2
-lib/R/NEWS.pdf
 lib/R/SVN-REVISION
 lib/R/bin/BATCH
 lib/R/bin/COMPILE
@@ -53,6 +42,11 @@ lib/R/doc/CRAN_mirrors.csv
 lib/R/doc/FAQ
 lib/R/doc/KEYWORDS
 lib/R/doc/KEYWORDS.db
+lib/R/doc/NEWS
+lib/R/doc/NEWS.0
+lib/R/doc/NEWS.1
+lib/R/doc/NEWS.2
+lib/R/doc/NEWS.pdf
 lib/R/doc/NEWS.rds
 lib/R/doc/RESOURCES
 lib/R/doc/THANKS
@@ -78,6 +72,12 @@ lib/R/doc/manual/R-exts.html
 lib/R/doc/manual/R-intro.html
 lib/R/doc/manual/R-ints.html
 lib/R/doc/manual/R-lang.html
+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/etc/Makeconf
 lib/R/etc/Renviron
 lib/R/etc/javaconf
@@ -96,6 +96,7 @@ lib/R/include/R_ext/Error.h
 lib/R/include/R_ext/GetX11Image.h
 lib/R/include/R_ext/GraphicsDevice.h
 lib/R/include/R_ext/GraphicsEngine.h
+lib/R/include/R_ext/Itermacros.h
 lib/R/include/R_ext/Lapack.h
 lib/R/include/R_ext/Linpack.h
 lib/R/include/R_ext/MathThreads.h
@@ -107,6 +108,7 @@ lib/R/include/R_ext/QuartzDevice.h
 lib/R/include/R_ext/R-ftp-http.h
 lib/R/include/R_ext/RS.h
 lib/R/include/R_ext/RStartup.h
+lib/R/include/R_ext/Rallocators.h
 lib/R/include/R_ext/Random.h
 lib/R/include/R_ext/Rdynload.h
 lib/R/include/R_ext/Riconv.h
@@ -147,6 +149,7 @@ lib/R/library/KernSmooth/html/R.css
 lib/R/library/KernSmooth/libs/KernSmooth.so
 lib/R/library/KernSmooth/po/de/LC_MESSAGES/R-KernSmooth.mo
 lib/R/library/KernSmooth/po/en@quot/LC_MESSAGES/R-KernSmooth.mo
+lib/R/library/KernSmooth/po/fr/LC_MESSAGES/R-KernSmooth.mo
 lib/R/library/KernSmooth/po/ko/LC_MESSAGES/R-KernSmooth.mo
 lib/R/library/KernSmooth/po/pl/LC_MESSAGES/R-KernSmooth.mo
 lib/R/library/MASS/CITATION
@@ -262,6 +265,7 @@ lib/R/library/Matrix/po/de/LC_MESSAGES/Matrix.mo
 lib/R/library/Matrix/po/de/LC_MESSAGES/R-Matrix.mo
 lib/R/library/Matrix/po/en@quot/LC_MESSAGES/Matrix.mo
 lib/R/library/Matrix/po/en@quot/LC_MESSAGES/R-Matrix.mo
+lib/R/library/Matrix/po/fr/LC_MESSAGES/R-Matrix.mo
 lib/R/library/Matrix/po/pl/LC_MESSAGES/Matrix.mo
 lib/R/library/Matrix/po/pl/LC_MESSAGES/R-Matrix.mo
 lib/R/library/Matrix/test-tools-1.R
@@ -303,6 +307,7 @@ lib/R/library/boot/NAMESPACE
 lib/R/library/boot/R/boot
 lib/R/library/boot/R/boot.rdb
 lib/R/library/boot/R/boot.rdx
+lib/R/library/boot/bd.q
 lib/R/library/boot/data/Rdata.rdb
 lib/R/library/boot/data/Rdata.rds
 lib/R/library/boot/data/Rdata.rdx
@@ -371,6 +376,8 @@ lib/R/library/cluster/html/R.css
 lib/R/library/cluster/libs/cluster.so
 lib/R/library/cluster/po/de/LC_MESSAGES/R-cluster.mo
 lib/R/library/cluster/po/en@quot/LC_MESSAGES/R-cluster.mo
+lib/R/library/cluster/po/en@quot/LC_MESSAGES/cluster.mo
+lib/R/library/cluster/po/fr/LC_MESSAGES/R-cluster.mo
 lib/R/library/cluster/po/pl/LC_MESSAGES/R-cluster.mo
 lib/R/library/codetools/DESCRIPTION
 lib/R/library/codetools/INDEX
@@ -471,6 +478,10 @@ lib/R/library/grDevices/NAMESPACE
 lib/R/library/grDevices/R/grDevices
 lib/R/library/grDevices/R/grDevices.rdb
 lib/R/library/grDevices/R/grDevices.rdx
+lib/R/library/grDevices/afm/ArialMT-Bold.afm.gz
+lib/R/library/grDevices/afm/ArialMT-BoldItalic.afm.gz
+lib/R/library/grDevices/afm/ArialMT-Italic.afm.gz
+lib/R/library/grDevices/afm/ArialMT.afm.gz
 lib/R/library/grDevices/afm/CM_boldx_10.afm.gz
 lib/R/library/grDevices/afm/CM_boldx_italic_10.afm.gz
 lib/R/library/grDevices/afm/CM_italic_10.afm.gz
@@ -635,6 +646,7 @@ lib/R/library/grid/NAMESPACE
 lib/R/library/grid/R/grid
 lib/R/library/grid/R/grid.rdb
 lib/R/library/grid/R/grid.rdx
+lib/R/library/grid/doc/DivByZero.txt
 lib/R/library/grid/doc/changes.txt
 lib/R/library/grid/doc/displaylist.pdf
 lib/R/library/grid/doc/frame.pdf
@@ -691,7 +703,7 @@ lib/R/library/lattice/po/de/LC_MESSAGES/R-lattice.mo
 lib/R/library/lattice/po/en@quot/LC_MESSAGES/R-lattice.mo
 lib/R/library/lattice/po/fr/LC_MESSAGES/R-lattice.mo
 lib/R/library/lattice/po/ko/LC_MESSAGES/R-lattice.mo
-lib/R/library/lattice/po/pl_PL/LC_MESSAGES/R-lattice.mo
+lib/R/library/lattice/po/pl/LC_MESSAGES/R-lattice.mo
 lib/R/library/methods/DESCRIPTION
 lib/R/library/methods/INDEX
 lib/R/library/methods/Meta/Rd.rds
@@ -1126,6 +1138,7 @@ lib/R/library/translations/de/LC_MESSAGES/splines.mo
 lib/R/library/translations/de/LC_MESSAGES/stats.mo
 lib/R/library/translations/de/LC_MESSAGES/tcltk.mo
 lib/R/library/translations/de/LC_MESSAGES/tools.mo
+lib/R/library/translations/de/LC_MESSAGES/utils.mo
 lib/R/library/translations/en/LC_MESSAGES/R.mo
 lib/R/library/translations/en@quot/LC_MESSAGES/R-base.mo
 lib/R/library/translations/en@quot/LC_MESSAGES/R-compiler.mo
diff --git a/math/R/distinfo b/math/R/distinfo
index 445776b3ef1..3e783dafd31 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.58 2014/03/14 20:15:38 markd Exp $
+$NetBSD: distinfo,v 1.59 2014/05/03 22:29:42 markd Exp $
 
-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 (R-3.1.0.tar.gz) = a9d13932c739cc12667c6a17fabd9361624a1708
+RMD160 (R-3.1.0.tar.gz) = 15d6c762baf36d4e2680599b5e976d0c068b7dbd
+Size (R-3.1.0.tar.gz) = 28469975 bytes
 SHA1 (patch-ac) = cbfe9853a6b1bdfa68d21c0a291f39545b131333
-SHA1 (patch-ad) = 21c2f74ceb41afa72b0b268ba4b1dcb57f01e106
+SHA1 (patch-ad) = b40536fac079e2cc348a020fafac687f2f8b1dfe
diff --git a/math/R/patches/patch-ad b/math/R/patches/patch-ad
index 1c1ed9c34eb..80ff8237e4a 100644
--- a/math/R/patches/patch-ad
+++ b/math/R/patches/patch-ad
@@ -1,10 +1,10 @@
-$NetBSD: patch-ad,v 1.16 2013/08/13 19:53:30 markd Exp $
+$NetBSD: patch-ad,v 1.17 2014/05/03 22:29:42 markd Exp $
 Adjust EXTRA_LIBS and @WANT_R_SHLIB_TRUE@R_bin_LDADD
 
---- src/main/Makefile.in.orig	2013-03-05 23:02:40.000000000 +0000
+--- src/main/Makefile.in.orig	2014-04-13 11:25:39.000000000 +0000
 +++ src/main/Makefile.in
-@@ -95,13 +95,13 @@ EXTRA_STATIC_LIBS = \
-   $(R_ZLIBS) $(R_BZLIBS) $(R_PCRE) $(R_TRE) $(R_XDR) $(R_XZ) $(R_LIBINTL)
+@@ -98,13 +98,13 @@ EXTRA_STATIC_LIBS = \
+   $(R_ZLIBS) $(R_BZLIBS) $(R_PCRE) $(R_TRE) $(R_XDR) $(R_XZ) $(R_LIBINTL) $(R_TZONE)
  STATIC_LIBS = $(MAIN_LIBS) $(EXTRA_STATIC_LIBS)
  
 -EXTRA_LIBS = $(BLAS_LIBS) $(FLIBS) $(R_XTRA_LIBS) @LIBINTL@ $(READLINE_LIBS) $(LIBS)