CVS log for pkgsrc/math/R/PLIST

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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

Add BUILD_DEPENDS on some TeX components so that NEWS.pdf is successfully
built.  Fix PLIST.  Bump PKGREVISION.

Update R to 2.14.0

changes to many to list - see NEWS file in distribution for details.

Changes 2.11.0:
* Packages must have been installed under R >= 2.10.0, as the
  current help system is the only one now supported.
* A port to 64-bit Windows is now available as well as binary package
  repositiories: see the 'R Administration and Installation Manual'.
* Argument matching for primitive functions is now done in the same way
  as for interpreted functions except for the deliberate exceptions
	call switch .C .Fortran .Call .External
  all of which use positional matching for their first argument,
  and also some internal-use-only primitives.
* The default device for command-line R at the console on Mac OS X
  is now quartz() and not X11().

New features
* The 'open' modes for connections are now interpreted more consistently.
* R CMD INSTALL now uses the internal untar() in package utils.
* help(try.all.packages = TRUE) is much faster.
* R CMD check has a new option '--timings' to record per-example timings
  in file <pkg>.Rcheck/<pkg>-Ex.timings.
* The TRE library has been updated to version 0.8.0 (minor bugfixes).
More...

Changes 2.10.0:
* Package help is now converted from Rd by the R-based converters
  that were first introduced in 2.9.0.
* HTML help is now generated dynamically using an HTTP server
  running in the R process and listening on the loopback interface.
* polygon(), pdf() and postscript() now have a parameter
  'fillOddEven' (default FALSE), which controls the mode used for
  polygon fills of self-intersecting shapes.
* New debugonce() function; further,
  getOption("deparse.max.lines") is now observed when debugging.
* plot() methods for "stepfun" and hence "ecdf" no longer plot
  points by default for n >= 1000.
* [g]sub(*, perl=TRUE) now also supports '\E' in order to *end*
  \U and \L case changes, thanks to a patch from Bill Dunlap.
* factor(), `levels<-`(), etc, now ensure that the resulting factor
  levels are unique (as was always the implied intention).  Factors
  with duplicated levels are still constructible by low-level means,
  but are now declared illegal.
* New print() (S3) method for class "function", also used for
  auto-printing.  Further, .Primitive functions now print and
  auto-print identically.
* The print() and toLatex() methods for class "sessionInfo" now
  show the locale in a nicer format and have arguments to
  suppress locale information.
* In addition to previously only round(), there are other 'Math'
  group (S3) methods for 'difftime', such as floor(), signif(), abs(), etc.
* For completeness, old.packages() and available.packages() allow
  'type' to be specified (you could always specify 'available'
  or 'contriburl').
* More...

Remove @dirrm entries from PLISTs

Update to R 2.7.2

NEW FEATURES

    o   sprintf() returns elements of the result in UTF-8 when the
        format or any character input has a corresponding element
        declared as UTF-8.  Similarly for paste(), elements of the
        result are in UTF-8 when any input to that element is declared
        as UTF-8.

    o   axis() has new arguments 'col.ticks' and 'lwd.ticks' to allow
        the colour and line width of ticks to be set separately from
        that of the line (e.g. to set one or the other to transparent
        or zero width).

    o   legend() has a new argument 'box.col' to set the colour of the
        enclosing box.

    o   legend() gains a 'xpd' argument to make it easier to place a
        legend in the margins or outer margins.

    o   stripchart() now passes '...' to title() (as well as to
        plot.default() and axis()). (Wish of PR#12202)

    o   help.search() has new argument 'searchEngine' to go
        directly to the search form: this is needed by users of
        Firefox 3 to workaround a bug in interpreting the search
        results pages.

+ BUG FIXES

2.7.1 NEW FEATURES

    o   tools::texi2dvi() has a new argument 'texinputs' to allow the
        TeX and bibtex input paths to be specified (even on MiKTeX).

    o   dev.copy2pdf() gains an 'out.type' argument to allow it to be
        used with cairo_pdf() or quartz(type = "pdf").

    o   poly() has additional checks against user error (as in PR#11243).

    o   The Mac OS quartz() device draws contiguous lines much faster.

    o   A field containing just a sign is no longer regarded as numeric
        (it was on all platforms in 2.7.0, but not on most in earlier
        versions of R).  Similarly, '.' is now always non-numeric.

    o   CITATION files are now read in Latin-1: quite a few were
        failing if used in a multibyte locale such as UTF-8.

    o   The DESCRIPTION file of a package can specify an 'OS_type' field
        as either 'unix' or 'windows' to confine installation to that
        OS type.

    o   HoltWinters() now uses optimize() rather than optim for
        one-parameter problems which should be more reliable (PR#11469).

    o   axis() now respects the setting of par("xpd") when clipping.

    o   The 'factor' method of format() now preserves names, dims and
        dimnames in the same way as for character and numeric inputs.
        (PR#11512)

    o   read.DIF(*, transpose=TRUE) now allows to correctly read DIF files
        produced by some versions of Excel.

DEPRECATED & DEFUNCT

    o   The use of unserialize() on character strings is deprecated:
        that was a format used in R < 2.4.0.

    o   The use of embedded nuls in character strings is deprecated:
        They will no longer be allowed in R 2.8.0.


UTILITIES

    o   R CMD check checks for possible check directories in the
        sources -- in mid-2008 there were about 20 examples on CRAN.

    o   R CMD build tries harder to clean up the inst/doc directory
        from the remnants of earlier builds.

        It also removes any directories with extension .Rcheck, and
        files .DS_Store and ._* (created by tar on Mac OS X under some
        circumstances: it now sets environment variables to ask for
        such files not to be created by that tar.)


+ BUG FIXES

Update to 2.7.0

SIGNIFICANT USER-VISIBLE CHANGES

    o   The default graphics device in non-interactive use is now
        pdf() rather than postscript().  [PDF viewers are now
        more widely available than PostScript viewers.]

        The default width and height for pdf() and bitmap() have been
        changed to 7 (inches) to match the screen devices.

    o   Most users of the X11() device will see a new device that has
        different fonts, anti-aliasing of lines and fonts and
        supports semi-transparent colours.

    o   Considerable efforts have been made to make the default output
        from graphics devices as similar as possible (and in
        particular close to that from postscript/pdf).  Many devices
        were misinterpreting 'pointsize' in some way, for example as
        being in device units (pixels) rather than in points.

    o   Packages which include graphics devices need to be re-installed
        for this version of R, with recently updated versions.

+ New features and bug fixes.

Update to R 2.6.2.

Changes are basically bugfixes.

pkgsrc changes:
  Don't bother patching configure.ac - it was only part of the changes
being made to configure so don't pretend you could use it to regerate
configure.
  Use -fPIC rather than -fpic for NetBSD powerpc.  Should fix PR 38032.

Update R to version 2.6.0

Many new features, changes and bug fixes. See lib/R/doc/NEWS for details.

Fix configure's handling of libblas when compiling with f2c and therefore
remove conditional PLIST entry no longer required. Bump PKGREVISION.

Building with f2c effects what libs get installed. Adjust PLIST.

Update R to version 2.4.1.

pkgsrc changes: no longer automatically generate the PLIST.
     use (de)install templates for handling updating the index files
     when adding/removing R packages.

Changes 2.4.1
This is a maintenance release and fixes a number of mostly minor bugs.

Changes 2.4.0
This release has many new features. One important aspect is that S4
classes now have their own internal type, and S4 method dispatch has
been completely revised to using cached generic functions, giving
substantial performance improvements. As a consequence, all packages
depending on "methods" need to be reinstalled.

Move pkg/ files into package's toplevel directory