[pkgsrc/trunk]: pkgsrc/math/R Update to 3.3.2

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

details:   https://anonhg.NetBSD.org/pkgsrc/rev/85ea6abd956a
branches:  trunk
changeset: 354639:85ea6abd956a
user:      wen <wen%pkgsrc.org@localhost>
date:      Sun Nov 06 02:08:16 2016 +0000

description:
Update to 3.3.2

Upstream changes:
CHANGES IN R 3.3.2:

  NEW FEATURES:

    * extSoftVersion() now reports the version (if any) of the readline
      library in use.

    * The version of LAPACK included in the sources has been updated to
      3.6.1, a bug-fix release including a speedup for the
      non-symmetric case of eigen().

    * Use options(deparse.max.lines=) to limit the number of lines
      recorded in .Traceback and other deparsing activities.

    * format(<AsIs>) looks more regular, also for non-character atomic
      matrices.

    * abbreviate() gains an option named = TRUE.

    * The online documentation for package methods is extensively
      rewritten.  The goals are to simplify documentation for basic
      use, to note old features not recommended and to correct
      out-of-date information.

    * Calls to setMethod() no longer print a message when creating a
      generic function in those cases where that is natural: S3
      generics and primitives.

  INSTALLATION and INCLUDED SOFTWARE:

    * Versions of the readline library >= 6.3 had been changed so that
      terminal window resizes were not signalled to readline: code has
      been added using a explicit signal handler to work around that
      (when R is compiled against readline >= 6.3).  (PR#16604)

    * configure works better with Oracle Developer Studio 12.5.

  UTILITIES:

    * R CMD check reports more dubious flags in files
      src/Makevars[.in], including -w and -g.

    * R CMD check has been set up to filter important warnings from
      recent versions of gfortran with -Wall -pedantic: this now
      reports non-portable GNU extensions such as out-of-order
      declarations.

    * R CMD config works better with paths containing spaces, even
      those of home directories (as reported by Ken Beath).

  DEPRECATED AND DEFUNCT:

    * Use of the C/C++ macro NO_C_HEADERS is deprecated (no C headers
      are included by R headers from C++ as from R 3.3.0, so it should
      no longer be needed).

  BUG FIXES:

    * The check for non-portable flags in R CMD check could be stymied
      by src/Makevars files which contained targets.

    * (Windows only) When using certain desktop themes in Windows 7 or
      higher, Alt-Tab could cause Rterm to stop accepting input.
      (PR#14406; patch submitted by Jan Gleixner.)

    * pretty(d, ..) behaves better for date-time d (PR#16923).

    * When an S4 class name matches multiple classes in the S4 cache,
      perform a dynamic search in order to obey namespace imports.
      This should eliminate annoying messages about multiple hits in
      the class cache.  Also, pass along the package from the
      ClassExtends object when looking up superclasses in the cache.

    * sample(NA_real_) now works.

    * Packages using non-ASCII encodings in their code did not install
      data properly on systems using different encodings.

    * merge(df1, df2) now also works for data frames with column names
      "na.last", "decreasing", or "method".  (PR#17119)

    * contour() caused a segfault if the labels argument had length
      zero.  (Reported by Bill Dunlap.)

    * unique(warnings()) works more correctly, thanks to a new
      duplicated.warnings() method.

    * findInterval(x, vec = numeric(), all.inside = TRUE) now returns
      0s as documented.  (Reported by Bill Dunlap.)

    * (Windows only) R CMD SHLIB failed when a symbol in the resulting
      library had the same name as a keyword in the .def file.
      (PR#17130)

    * pmax() and pmin() now work with (more ?)  classed objects, such
      as "Matrix" from the Matrix package, as documented for a long
      time.

    * axis(side, x = D) and hence Axis() and plot() now work correctly
      for "Date" and time objects D, even when "time goes backward",
      e.g., with decreasing xlim.  (Reported by William May.)

    * str(I(matrix(..))) now looks as always intended.

    * plot.ts(), the plot() method for time series, now respects cex,
      lwd and lty.  (Reported by Greg Werbin.)

    * parallel::mccollect() now returns a named list (as documented)
      when called with wait = FALSE.  (Reported by Michel Lang.)

    * If a package added a class to a class union in another package,
      loading the first package gave erroneous warnings about
      "undefined subclass".

    * c()'s argument use.names is documented now, as belonging to the
      (C internal) default method.  In "parallel", argument recursive
      is also moved from the generic to the default method, such that
      the formal argument list of base generic c() is just (...).

    * rbeta(4, NA) and similarly rgamma() and rnbinom() now return
      NaN's with a warning, as other r<dist>(), and as documented.
      (PR#17155)

    * Using options(checkPackageLicense = TRUE) no longer requires
      acceptance of the licence for non-default standard packages such
      as compiler.  (Reported by Mikko Korpela.)

    * split(<very_long>, *) now works even when the split off parts are
      long. (PR#17139)

    * min() and max() now also work correctly when the argument list
      starts with character(0).  (PR#17160)

    * Subsetting very large matrices (prod(dim(.)) >= 2^31) now works
      thanks to Michael Schubmehl's PR#17158.

    * bartlett.test() used residual sums of squares instead of
      variances, when the argument was a list of lm objects.  (Reported
      by Jens Ledet Jensen).

    * plot(<lm>, which = *) now correctly labels the contour lines for
      the standardized residuals for which = 6.  It also takes the
      correct p in case of singularities (also for which = 5).
      (PR#17161)

    * xtabs(~ exclude) no longer fails from wrong scope, thanks to
      Suharto Anggono's PR#17147.

    * Reference class calls to methods() did not re-analyse previously
      defined methods, meaning that calls to methods defined later
      would fail. (Reported by Charles Tilford).

    * findInterval(x, vec, left.open = TRUE) misbehaved in some cases.
      (Reported by Dmitriy Chernykh.)

diffstat:

 math/R/Makefile |   5 ++---
 math/R/distinfo |  10 +++++-----
 2 files changed, 7 insertions(+), 8 deletions(-)

diffs (31 lines):

diff -r dd0bb4ce66e8 -r 85ea6abd956a math/R/Makefile
--- a/math/R/Makefile   Sun Nov 06 00:34:10 2016 +0000
+++ b/math/R/Makefile   Sun Nov 06 02:08:16 2016 +0000
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.169 2016/10/07 18:25:59 adam Exp $
+# $NetBSD: Makefile,v 1.170 2016/11/06 02:08:16 wen Exp $
 
-DISTNAME=              R-3.3.1
-PKGREVISION=           1
+DISTNAME=              R-3.3.2
 CATEGORIES=            math
 MASTER_SITES=          ${MASTER_SITE_R_CRAN:=base/R-3/}
 
diff -r dd0bb4ce66e8 -r 85ea6abd956a math/R/distinfo
--- a/math/R/distinfo   Sun Nov 06 00:34:10 2016 +0000
+++ b/math/R/distinfo   Sun Nov 06 02:08:16 2016 +0000
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.73 2016/07/26 04:53:33 wen Exp $
+$NetBSD: distinfo,v 1.74 2016/11/06 02:08:16 wen Exp $
 
-SHA1 (R-3.3.1.tar.gz) = df853188d3e2b1c2d32393016401c432a5192c4d
-RMD160 (R-3.3.1.tar.gz) = 200071bfb126195f7bbc56ad7678227274d72f5b
-SHA512 (R-3.3.1.tar.gz) = d0ff85e99b9ec9cac672aa30d7d1a854778c6a610bcc5336e8c60c8c74f20856f2bfeae085af793fad646ff45cb4677d9d6dcbaa18212591f72f00a02339f4cd
-Size (R-3.3.1.tar.gz) = 29848329 bytes
+SHA1 (R-3.3.2.tar.gz) = 0e39e9c2d28fe6bab9c55ca23e08ba8727fd2fca
+RMD160 (R-3.3.2.tar.gz) = 99eb136e8ffb6f4a09943565af08f3dd4a5a7491
+SHA512 (R-3.3.2.tar.gz) = 06a98687c0b180cb0bfd57440ea26088212d9f48948d503136475bf54b42d72cfec5bea7e333c0cedd60733bd614dd0f8c2eced7e24478b6c89f48e8d0c43482
+Size (R-3.3.2.tar.gz) = 29440670 bytes
 SHA1 (patch-ac) = 68c1943a352e6f8b2842331578ed746b1ac27bea
 SHA1 (patch-ad) = a43b4875a2ee4677b5f762abf3f9a623fd12cbb5
 SHA1 (patch-src_include_GraphicsBase.h) = eed25eaca982ca76bf75d199dd8bf48be2a99ac5