CVS commit: pkgsrc/math/R

["Wen Heping" <wen%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wen
Date:           Fri Aug 14 12:40:20 UTC 2015

Modified Files:
        pkgsrc/math/R: Makefile PLIST distinfo
        pkgsrc/math/R/patches: patch-ac

Log Message:
Update to 3.2.2

Upstream changes:
CHANGES IN R 3.2.2:

  SIGNIFICANT USER-VISIBLE CHANGES:

    * It is now easier to use secure downloads from https:// URLs on
      builds which support them: no longer do non-default options need
      to be selected to do so.  In particular, packages can be
      installed from repositories which offer https:// URLs, and those
      listed by setRepositories() now do so (for some of their
      mirrors).

      Support for https:// URLs is available on Windows, and on other
      platforms if support for libcurl was compiled in and if that
      supports the https protocol (system installations can be expected
      to do).  So https:// support can be expected except on rather old
      OSes (an example being OS X 'Snow Leopard', where a non-system
      version of libcurl can be used).

      (Windows only) The default method for accessing URLs _via_
      download.file() and url() has been changed to be "wininet" using
      Windows API calls.  This changes the way proxies need to be set
      and security settings made: there have been some reports of sites
      being inaccessible under the new default method (but the previous
      methods remain available).

  NEW FEATURES:

    * cmdscale() gets new option list. for increased flexibility when a
      list should be returned.

    * configure now supports texinfo version 6.0, which (unlike the
      change from 4.x to 5.0) is a minor update.  (Wish of PR#16456.)

    * (Non-Windows only) download.file() with default method = "auto"
      now chooses "libcurl" if that is available and a https:// or
      ftps:// URL is used.

    * (Windows only) setInternet2(TRUE) is now the default.  The
      command-line option --internet2 and environment variable
      R_WIN_INTERNET2 are now ignored.

      Thus by default the "internal" method for download.file() and
      url() uses the "wininet" method: to revert to the previous
      default use setInternet2(FALSE).

      This means that https:// can be read by default by
      download.file() (they have been readable by file() and url()
      since R 3.2.0).

      There are implications for how proxies need to be set (see
      ?download.file): also, cacheOK = FALSE is not supported.

    * chooseCRANmirror() and chooseBioCmirror() now offer HTTPS mirrors
      in preference to HTTP mirrors.  This changes the interpretation
      of their ind arguments: see their help pages.

    * capture.output() gets optional arguments type and split to pass
      to sink(), and hence can be used to capture messages.

  C-LEVEL FACILITIES:

    * Header Rconfig.h now defines HAVE_ALLOCA_H if the platform has
      the alloca.h header (it is needed to define alloca on Solaris and
      AIX, at least: see 'Writing R Extensions' for how to use it).

  INSTALLATION and INCLUDED SOFTWARE:

    * The libtool script generated by configure has been modified to
      support FreeBSD >= 10 (PR#16410).

  BUG FIXES:

    * The HTML help page links to demo code failed due to a change in R
      3.2.0.  (PR#16432)

    * If the na.action argument was used in model.frame(), the original
      data could be modified. (PR#16436)

    * getGraphicsEvent() could cause a crash if a graphics window was
      closed while it was in use. (PR#16438)

    * matrix(x, nr, nc, byrow = TRUE) failed if x was an object of type
      "expression".

    * strptime() could overflow the allocated storage on the C stack
      when the timezone had a non-standard format much longer than the
      standard formats. (Part of PR#16328.)

    * options(OutDec = s) now signals a warning (which will become an
      error in the future) when s is not a string with exactly one
      character, as that has been a documented requirement.

    * prettyNum() gains a new option input.d.mark which together with
      other changes, e.g., the default for decimal.mark, fixes some
      format()ting variants with non-default getOption("OutDec") such
      as in PR#16411.

    * download.packages() failed for type equal to either "both" or
      "binary".  (Reported by Dan Tenenbaum.)

    * The dendrogram method of labels() is much more efficient for
      large dendrograms, now using rapply().  (Comment #15 of PR#15215)

    * The "port" algorithm of nls() could give spurious errors.
      (Reported by Radford Neal.)

    * Reference classes that inherited from reference classes in
      another package could invalidate methods of the inherited class.
      Fixing this requires adding the ability for methods to be
      "external", with the object supplied explicitly as the first
      argument, named .self. See "Inter-Package Superclasses" in the
      documentation.

    * readBin() could fail on the SPARC architecture due to alignment
      issues.  (Reported by Radford Neal.)

    * qt(*, df=Inf, ncp=.) now uses the natural qnorm() limit instead
      of returning NaN. (PR#16475)

    * Auto-printing of S3 and S4 values now searches for print() in the
      base namespace and show() in the methods namespace instead of
      searching the global environment.

    * polym() gains a coefs = NULL argument and returns class "poly"
      just like poly() which gets a new simple=FALSE option.  They now
      lead to correct predict()ions, e.g., on subsets of the original
      data.

    * rhyper(nn, <large>) now works correctly. (PR#16489)

    * ttkimage() did not (and could not) work so was removed. Ditto for
      tkimage.cget() and tkimage.configure(). Added two Ttk widgets and
      missing subcommands for Tk's image command: ttkscale(),
      ttkspinbox(), tkimage.delete(), tkimage.height(),
      tkimage.inuse(), tkimage.type(), tkimage.types(),
      tkimage.width(). (PR#15372, PR#16450)

    * getClass("foo") now also returns a class definition when it is
      found in the cache more than once.


To generate a diff of this commit:
cvs rdiff -u -r1.160 -r1.161 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.22 -r1.23 pkgsrc/math/R/PLIST
cvs rdiff -u -r1.68 -r1.69 pkgsrc/math/R/distinfo
cvs rdiff -u -r1.35 -r1.36 pkgsrc/math/R/patches/patch-ac

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.