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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

Recursive bump for pcre-8.30* (shlib major change)

Revbump for
a) tiff update to 4.0 (shlib major change)
b) glib2 update 2.30.2 (adds libffi dependency to buildlink3.mk)

Enjoy.

This needs a pile more tex packages to build successfully in a clean
environment. Note: some of the ones I'm adding may not be absolutely
required; I made this list by checking atimes after building R with
all tex stuff available, and confirmed that with (only) these packages
available it does build.

It doesn't help that the R makefile, apparently intentionally, doesn't
stop if running tex fails.

fix pasto

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

Cairo support needs pkg-config

s/fortran77/fortran/  as uses some features that f2c can't handle.

Update R to 2.14.0

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

Recursive bump for graphics/freetype2 buildlink addition.

Add LIBnn=lib to ./configure environment. This fixes a build failure on 64bit linux.

Briefly discussed with wiz@

recursive bump from gettext-lib shlib bump.

As suggested by joerg@, set PTHREAD_AUTO_VARS="yes". This fixes the issues
discussed in:

	http://mail-index.netbsd.org/pkgsrc-users/2011/01/24/msg013585.html

png shlib name changed for png>=1.5.0, so bump PKGREVISIONs.

Mechanically replace references to graphics/jpeg with the suitable
alternative from mk/jpeg.buildlink3.mk

This allows selection of an alternative jpeg library (namely the x86 MMX,
SSE, SSE2 accelerated libjpeg-turbo) via JPEG_DEFAULT=libjpeg-turbo, and
follows the current standard model for alternatives (fam, motif, fuse etc).

The mechanical edits were applied via the following script:

#!/bin/sh
for d in */*; do
  [ -d "$d" ] || continue
  for i in "$d/"Makefile* "$d/"*.mk; do
    case "$i" in *.orig|*"*"*) continue;; esac
    out="$d/x"
    sed -e 's;graphics/jpeg/buildlink3\.mk;mk/jpeg.buildlink3.mk;g' \
        -e 's;BUILDLINK_PREFIX\.jpeg;JPEGBASE;g' \
        < "$i" > "$out"
    if cmp -s "$i" "$out"; then
      rm -f "$out"
    else
      echo "Edited $i"
      mv -f "$i" "$i.orig" && mv "$out" "$i"
    fi
  done
done

Bump dependency on pixman to 0.18.4 because cairo-1.10 needs that
version, and bump all depends.

Per discussion on pkgsrc-changes.

"fortran" -> "fortran77" except where it is clear that it isn't F77.
"fortran" is alias of "fortran77" for now, but it will change later.

Changes 2.11.1:

* R CMD INSTALL checks if dependent packages are available early on
* in the installation of source packages, thereby giving clearer
  error messages.
* R CMD INSTALL --build now names the file in the format used
  for Mac OS X binary files on that platform.
* BIC() in package stats4 now also works with multiple fitted models,
  analogously to AIC().
* Use of file extension .C for C++ code in packages is now
  deprecated: it has caused problems for some 'make's on
  case-insensitive file systems (although it currently works
  with the recommended toolkits).
* The C function mkCharLenCE now no longer reads past 'len' bytes
  (unlikely to be a problem except in user code).
* On systems without any default LD_LIBRARY_PATH (not even
  /usr/local/lib), [DY]LIB_LIBRARY_PATH is now set without a trailing colon.
* More efficient utf8ToInt() on long multi-byte strings with
  many multi-byte characters.
* aggregate.ts() gave platform-depedent results due to rounding
  error for ndeltat != 1.
* package.skeleton() sometimes failed to fix filenames for .R or
  .Rd files to start with an alphanumeric.

Bump PKGREVISION for libpng shlib name change.
Also add some patches to remove use of deprecated symbols and fix other
problems when looking for or compiling against libpng-1.4.x.

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 2.10.1:
* The PCRE library has been updated to version 8.00.
* R CMD INSTALL has new options --no-R, --no-libs, --no-data,
  --no-help, --no-demo, --no-exec, and --no-inst to suppress
  installation of the specified part of the package.
* The documented line-length limit of 4095 bytes when reading
  from the console now also applies also to parse(file="")
  (which previously had a limit of around 1024 bytes).
* A Bioconductor mirror can be set for use by setRepositories()
  via the option "BioC_mirror".
* Double-clicking in a tk_select.list() list box now selects the item
  and closes the list box (as happens on the Windows select.list() widget).
* configure will be able to find a usable libtiff in some rare
  circumstances where it did not previously (where libtiff
  needed to be linked explicitly against -ljpeg).
* Making refman.pdf works around a problem with the indexing
  with hyperref 6.79d and later.
* The 'extended' argument is deprecated in strsplit(), grep(),
  grepl(), sub(), gsub(), regexpr() and gregexpr() (not just the
  value extended = FALSE) and will be removed in R 2.11.0.
* bug fixes

Second try at jpeg-8 recursive PKGREVISION bump.

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...

Follow f2c/libf2c split: bump revision of all packages
that list Fortran in used languages.

bump revision because of graphics/jpeg update

Recursive ABI depends update and PKGREVISION bump for readline-6.0 shlib
major change.

Reported by Robert Elz in PR 41345.

Pullup ticket #2513 - requested by markd
R: security patch

Revisions pulled up:
- math/R/Makefile		1.99
- math/R/distinfo		1.39
- math/R/patches/patch-ae	1.15
---
Module Name:	pkgsrc
Committed By:	markd
Date:		Sun Aug 31 12:33:53 UTC 2008

Modified Files:
	pkgsrc/math/R: Makefile distinfo
Added Files:
	pkgsrc/math/R/patches: patch-ae

Log Message:
Fix for http://secunia.com/advisories/31647/ from R svn.

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

Fix for http://secunia.com/advisories/31647/ from R svn.

set --disable-R-framework and --without-aqua
these options are only used by R.app on Mac OS X

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.

+ Remove modifications to configure.in and configure in patch-aa and
  patch-ac that altered the order in which the terminal library for
  readline was detected.  The termcap.buildlink3.mk file (included
  indirectly by readline/buildlink3.mk) will do the right thing by
  itself.

+ Modify the pkg-index.tmpl INSTALL script fragment: we can just use
  ${PKG_PREFIX} instead of substituting for @PREFIX@ everywhere.  Also
  refactor the commands to rebuild the package index into a shell
  function and give some indication to the user what is happening.

+ Remove chown operation in post-install that was basically
  cargo-culted from the very first version of R imported into pkgsrc.
  It's not necessary.

+ Support user-destdir installation.

Bump the PKGREVISION to 2.

Bump version or revision of all packages that have a runtime dependency
on gzip.

Update R to version 2.6.0

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

Fixed the path to unzip. PKGREVISION++

Wants at least version 4.7 of makeinfo to build the docs.  Bump pkgrev.

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.

Needs libXt explicitly.

Pullup ticket 1853 - requested by dmcmahill
portability fixes for R

Revisions pulled up:
- pkgsrc/math/R/Makefile			1.86

   Module Name:		pkgsrc
   Committed By:	dmcmahill
   Date:		Sun Oct  8 23:12:48 UTC 2006

   Modified Files:
   	pkgsrc/math/R: Makefile

   Log Message:
   The variable modifier $${dir#${PREFIX}/} is not portable so eliminate its
   use.  Fixes R packaging on solaris.

The variable modifier $${dir#${PREFIX}/} is not portable so eliminate its
use.  Fixes R packaging on solaris.

Update to R 2.3.1

This version contains several minor fixups and removes a couple of bad
bugs such as NA-handling of mean() for integer vectors.

Changes 2.3.0
This version contains several changes and additions, mostly incremental.

Fixed pkglint warnings.

Bump BUILDLINK_ABI_DEPENDS.png and PKGREVISION for png-1.2.9nb2 update.

Over 1200 files touched but no revisions bumped :)

RECOMMENDED is removed. It becomes ABI_DEPENDS.

BUILDLINK_RECOMMENDED.foo becomes BUILDLINK_ABI_DEPENDS.foo.

BUILDLINK_DEPENDS.foo becomes BUILDLINK_API_DEPENDS.foo.

BUILDLINK_DEPENDS does not change.

IGNORE_RECOMMENDED (which defaulted to "no") becomes USE_ABI_DEPENDS
which defaults to "yes".

Added to obsolete.mk checking for IGNORE_RECOMMENDED.

I did not manually go through and fix any aesthetic tab/spacing issues.

I have tested the above patch on DragonFly building and packaging
subversion and pkglint and their many dependencies.

I have also tested USE_ABI_DEPENDS=no on my NetBSD workstation (where I
have used IGNORE_RECOMMENDED for a long time). I have been an active user
of IGNORE_RECOMMENDED since it was available.

As suggested, I removed the documentation sentences suggesting bumping for
"security" issues.

As discussed on tech-pkg.

I will commit to revbump, pkglint, pkg_install, createbuildlink separately.

Note that if you use wip, it will fail!  I will commit to pkgsrc-wip
later (within day).

* Teach the tools framework how to supply the pkgsrc version of
  makeinfo if no native makeinfo executable exists.  Honor TEXINFO_REQD
  when determining whether the native makeinfo can be used.

* Remove USE_MAKEINFO and replace it with USE_TOOLS+=makeinfo.

* Get rid of all the "split" argument deduction for makeinfo since
  the PLIST module already handles varying numbers of split info files
  correctly.

NOTE: Platforms that have "makeinfo" in the base system should check
      that the makeinfo entries of pkgsrc/mk/tools.${OPSYS}.mk are
      correct.

Recursive revision bump / recommended bump for gettext ABI change.

If MANZ=yes was set then the subsequent USE_TOOLS+=gzip caused a gzip
link to appear in the tools directory and be picked up and embedded in
one of the installed scripts.  Since this package clearly uses gzip at
runtime add an explicit USE_TOOLS+=gzip:run and fixup the gzip path that
gets embedded.  Fixes PR pkg/32218.  Bump PKGREVISION.

Update R to 2.2.1

USER-VISIBLE CHANGES

    o   options("expressions") has been reduced to 1000: the limit
        of 5000 introduced in 2.1.0 was liable to give crashes from C
        stack overflow.


NEW FEATURES

    o   Use of 'pch' (e.g. in points) in the symbol font 5 is now
        interpreted in the single-byte encoding used by that font.
        Similarly, strwidth now recognizes that font 5 has a different
        encoding from that of the locale.  (These are likely to affect
        the answer only in MBCS locales such as UTF-8.)

    o   The URW font metrics have been updated to versions from late
        2002 which cover more glyphs, including Cyrillic.

    o   New postscript encodings for CP1250 (Windows East European),
        ISO Latin-7 (8859-13, Latvian, Lithuanian and Maori), Cyrillic
        (8859-5), KOI8-R, KOI8-U and CP1251.

    o   configure has more support for the Intel and Portland Group
        compilers on ix86 and x86_64 Linux.

    o   R CMD INSTALL will clean up if interrupted (e.g. by ctrl-C from
        the keyboard).

    o   There is now a comprehensive French translation of the messages,
        thanks to Philippe Grosjean.


DEPRECATED & DEFUNCT

    o   The undocumented use of atan() with two arguments is deprecated:
        instead use atan2() (as documented).

    o   The 'vfont' argument of axis() and mtext() is deprecated
        (it currently warns and does nothing).

    o   The function mauchley.test() is deprecated (was a misspelling)
        and replaced by mauchly.test()

Many BUG FIXES

Update R to 2.2.0

Changes:
 This version contains several changes and additions, mostly incremental.

Fixed pkglint warnings. The warnings are mostly quoting issues, for
example MAKE_ENV+=FOO=${BAR} is changed to MAKE_ENV+=FOO=${BAR:Q}. Some
other changes are outlined in

    http://mail-index.netbsd.org/tech-pkg/2005/12/02/0034.html

- correctly depend on devel/gettext-lib, bump revision for this
- this uses libtool, tell the framework so
- don't declare alloca on DragonFly, it conflicts with system headers
- patch libtool.m4 fragment for DrgaonFly

Replaced "# defined" with "yes" in Makefile variables like GNU_CONFIGURE,
NO_BUILD, USE_LIBTOOL.

add missing libiconv buildlink3.mk

Get rid of USE_PERL5.  The new way to express needing the Perl executable
around at either build-time or at run-time is:

	USE_TOOLS+=	perl		# build-time
	USE_TOOLS+=	perl:run	# run-time

Also remove some places where perl5/buildlink3.mk was being included
by a package Makefile, but all that the package wanted was the Perl
executable.

Update R to version 2.1.1.

minor bug fixes.

Prevent paths to the build directories from being included in the package.
Bump PKGREVISION.

Cleanup of tools paths appearing in installed files for the new tools
framework.  Bump PKGREVISION.

Massive cleanup of buildlink3.mk and builtin.mk files in pkgsrc.
Several changes are involved since they are all interrelated.  These
changes affect about 1000 files.

The first major change is rewriting bsd.builtin.mk as well as all of
the builtin.mk files to follow the new example in bsd.builtin.mk.
The loop to include all of the builtin.mk files needed by the package
is moved from bsd.builtin.mk and into bsd.buildlink3.mk.  bsd.builtin.mk
is now included by each of the individual builtin.mk files and provides
some common logic for all of the builtin.mk files.  Currently, this
includes the computation for whether the native or pkgsrc version of
the package is preferred.  This causes USE_BUILTIN.* to be correctly
set when one builtin.mk file includes another.

The second major change is teach the builtin.mk files to consider
files under ${LOCALBASE} to be from pkgsrc-controlled packages.  Most
of the builtin.mk files test for the presence of built-in software by
checking for the existence of certain files, e.g. <pthread.h>, and we
now assume that if that file is under ${LOCALBASE}, then it must be
from pkgsrc.  This modification is a nod toward LOCALBASE=/usr.  The
exceptions to this new check are the X11 distribution packages, which
are handled specially as noted below.

The third major change is providing builtin.mk and version.mk files
for each of the X11 distribution packages in pkgsrc.  The builtin.mk
file can detect whether the native X11 distribution is the same as
the one provided by pkgsrc, and the version.mk file computes the
version of the X11 distribution package, whether it's built-in or not.

The fourth major change is that the buildlink3.mk files for X11 packages
that install parts which are part of X11 distribution packages, e.g.
Xpm, Xcursor, etc., now use imake to query the X11 distribution for
whether the software is already provided by the X11 distribution.
This is more accurate than grepping for a symbol name in the imake
config files.  Using imake required sprinkling various builtin-imake.mk
helper files into pkgsrc directories.  These files are used as input
to imake since imake can't use stdin for that purpose.

The fifth major change is in how packages note that they use X11.
Instead of setting USE_X11, package Makefiles should now include
x11.buildlink3.mk instead.  This causes the X11 package buildlink3
and builtin logic to be executed at the correct place for buildlink3.mk
and builtin.mk files that previously set USE_X11, and fixes packages
that relied on buildlink3.mk files to implicitly note that X11 is
needed.  Package buildlink3.mk should also include x11.buildlink3.mk
when linking against the package libraries requires also linking
against the X11 libraries.  Where it was obvious, redundant inclusions
of x11.buildlink3.mk have been removed.

Remove USE_GNU_TOOLS and replace with the correct USE_TOOLS definitions:

	USE_GNU_TOOLS	-> USE_TOOLS
	awk		-> gawk
	m4		-> gm4
	make		-> gmake
	sed		-> gsed
	yacc		-> bison

For packages that use GNU configure, don't bother adding "TOOL"
variables into CONFIGURE_ENV if the new tools framework already takes
care of adding them automatically.

Don't try and use wide chars on NetBSD 1.6 as the support isn't complete
enough.  Fixes PR pkg/30274

update to 2.1.0
too many changes to list here
...still doesn't work within TEXmacs

Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.

Move buildlink3.mk files ahead of targets as per example Makefile.

Fix up the comment to note that we still need to unwrap some files at
post-configure time, even after the switch from buildlink2 to buildlink3.
Also, use SUBST_CLASSES instead of the custom post-configure target,
and take advantage of the fact that the "unwrap" SUBST_CLASS already
does mostly the right thing.

Nuke USE_FORTRAN and bring the f2c handling within the mk/compiler
framework.  The list of changes include:

  * Modify compiler.mk so that "c" is always prepended to USE_LANGUAGES,
    so we no longer need to say it in package Makefiles.  Packages
    should now append to USE_LANGUAGES instead of setting it.

  * Create mk/compiler/f2c.mk which implements another pseudo-compiler
    "f2c" that may be used with any C compiler backend, e.g.

	PKGSRC_COMPILER= f2c ccache gcc

  * Teach the various "real" compiler files, e.g., sunpro.mk, mipspro.mk,
    etc., to use f2c if the native Fortran compiler isn't present.

Packages that use Fortran should now simply include the line:

	USE_LANGUAGES+=	fortran

in the package Makefile.

Update R to 2.0.1

Changes 2.0.1:
This is a maintenance version mainly to fix a number of minor bugs and
issues. Some rather nasty bugs were Windows-specific.

Changes 2.0.0:
Many things have changed since 1.0. The R language has acquired namespaces,
exception handling constructs, formal methods and classes, much improved
garbage collection, generalized I/O via connection objects, and
considerable improvements in the graphics area. The user workspace has been
reorganized, and so has the set of packages that ship with R. Several
"recommended packages" deemed indispensable in a statistical system are
bundled. In addition, there has been a large number of more specific new
functions, tweaks, and bugfixes.

USE_BUILDLINK3 is a yes/no variable.

Libtool fix for PR pkg/26633, and other issues.  Update libtool to 1.5.10
in the process.  (More information on tech-pkg.)

Bump PKGREVISION and BUILDLINK_DEPENDS of all packages using libtool and
installing .la files.

Bump PKGREVISION (only) of all packages depending directly on the above
via a buildlink3 include.

Annotate a comment:
# XXX: following comment still true for buildlink3?
# R does ugly things in the configure to get the default list of arguments
# for linking Fortran, which exposes the buildlink2 tricks so clean up
# afterwards

Update R to 1.9.1

CHANGES IN R VERSION 1.9.1


NEW FEATURES

    o   as.Date() now has a method for "POSIXlt" objects.

    o   mean() has a method for "difftime" objects and so summary()
        works for such objects.

    o   legend() has a new argument 'pt.cex'.

    o   plot.ts() has more arguments, particularly 'yax.flip'.

    o   heatmap() has a new 'keep.dendro' argument.

    o   The default barplot method now handles vectors and 1-d arrays
        (e.g., obtained by table()) the same, and uses grey instead of
        heat color palettes in these cases.  (Also fixes PR#6776.)

    o   nls() now looks for variables and functions in its formula in
        the environment of the formula before the search path, in the
        same way lm() etc look for variables in their formulae.


DEPRECATED & DEFUNCT

    o   Support for non-IEEE-754 arithmetic (which has been untested
        for some time) will be removed in the next full release.

    o   Direct use of R INSTALL|REMOVE|BATCH|COMPILE|SHLIB is
        deprecated: use R CMD instead.

    o   The gnome/GNOME graphics device is deprecated and will be
        removed in the next full release.

Plus Bug Fixes.

Enable pkgviews installation.

R assumes it can append to the DESCRIPTION files of each R package while
building even though it uses INSTALL_DATA on them so set SHAREMODE=644
rather than have to patch an ever increasing number of files.
Idea from Julio M. Merino Vidal.

Update R to 1.9.0 and buildlink3ify

USER-VISIBLE CHANGES

    o   Underscore '_' is now allowed in syntactically valid names, and
        make.names() no longer changes underscores.  Very old code
        that makes use of underscore for assignment may now give
        confusing error messages.

    o   Package 'base' has been split into packages 'base', 'graphics',
        'stats' and 'utils'.  All four are loaded in a default
        installation, but the separation allows a 'lean and mean'
        version of R to be used for tasks such as building indices.

        Packages ctest, eda, modreg, mva, nls, stepfun and ts have been
        merged into stats, and lqs has been returned to MASS.  In all
        cases a stub has been left that will issue a warning and ensure
        that the appropriate new home is loaded.  All the time series
        datasets have been moved to package stats.  Sweave has been
        moved to utils.

        Package mle has been moved to stats4 which will become the
        central place for statistical S4 classes and methods
        distributed with base R.  Package mle remains as a stub.

        Users may notice that code in .Rprofile is run with only the
        new base loaded and so functions may now not be found.  For
        example, ps.options(horizontal = TRUE) should be preceded by
        library(graphics) or called as graphics::ps.options or,
        better, set as a hook -- see ?setHook.

    o   There has been a concerted effort to speed up the startup of
        an R session: it now takes about 2/3rds of the time of 1.8.1.

    o   A warning is issued at startup in a UTF-8 locale, as currently R
        only supports single-byte encodings.

plus many new features and bug fixes.

Switch to using tk8.4
bump PKGREVISION

Enable tk84 and replace x11/tk with x11/tk83.  Packages compatible
with 8.4 will be updated to depend on x11/tk after Tk update.

USE_LANGUAGES= c fortran

replace deprecated USE_GMAKE with USE_GNU_TOOLS+=make.

Reintroduce reordering tests for termcap vs termlib vs ncurses and
make dependency on libbz2 explicit

Fixes build on Solaris 8.

Now uses shared blas library from math/blas

Update R to 1.8.1.

Changes since 1.6.2

Many new features.
Language changes.
Additional standard package 'mle'.
Some old features deprecated or defunct.
Many many bug fixes.

Update to 1.8.0 from Ray Brownrigg in private communication, cleaned up
and updated to 1.8.1 by me.

s/netbsd.org/NetBSD.org/

Make this relay on blas 1.0nb1 and use libblas_pic.a instead of libblas.a so
proper PIC objects get pulled into the .so's

Update to R-1.6.2

   CHANGES IN R VERSION 1.6.2

BUG FIXES

    o   plot.stepfun() now obeys a `ylim=.' specification.

    o   removeClass() does a better job of removing inheritance
        information.

    o   setIs() will not allow mismatched representations between two
        classes (without an explicit coerce method).

    o   The code underlying polygon drawing contained a memory leak.
        This showed up in persp, but did not affect other graphics
        functions.  It is now possible to draw big DEMs.

    o   logLik.nls() gave wrong df.

    o   rbind() with a mixture of data frames and matrices treated the
        matrices as vectors.

    o   stripchart(method="stack") was not handling missing values.

    o   Arithmetic functions such as log() lost the object bit from
        classed objects if coercion was needed.

    o   exp_rand would go into an infinite loop if unif_rand returned 0.

    o   formatC(x, format="fg") could return exponential format if
        rounding pushed x over a positive power of 10.

    o   attr(x, foo) used partial matching for `foo' (even though not
        documented to do so), and failed to find `foo' if there were
        two or more partial matches before the exact match in the list
        of attributes.

    o   Rdconv now creates direct HTML hyperlinks when linking to
        documentation in the same package.  The code now ensures that
        links which can be resolved within the package are so resolved,
        even when there are possible resolutions in other packages.

    o   If readBin(what=character()) is used incorrectly on a file which
        does not contain C-style character strings, warnings (usually
        many) are now given.

    o   Building libR.so with the zlib in the R sources was not
        finding the local zlib headers.

    o   system(intern=TRUE) has an undocumented line length limit of
        119 chars both on Unix and Windows.  The limit is now 8096 and
        documented.  On Unix (only) every 120th character used to be
        discarded.

    o   plot.POSIX[cl]t were not passing graphics parameters on to
        axis.POSIXct.

    o   On some HP-UX systems, installed scripts were not executable
        when using the BSD-compatible install system program found by
        configure.  We now always use install-sh on HP-UX.

    o   c() was converting NA names to "NA": now proper NA strings are
        used wherever possible.

    o   A typo was causing segfaults when using data.entry under SuSE.

Update R to version 1.6.1.

Pkgsrc changes:
Now builds the libR.so and provides a buildlink2.mk for packages that want
to use it.  From suggestions from Kent Polk.

Recommended library set is now included in the base package.

Changes:
               CHANGES IN R VERSION 1.6.1

NEW FEATURES

    o   Added a few "trivial and obviously missing" functions to tcltk:
        tkchooseDirectory, tkpopup, tkdialog, tkread

    o   barplot() has a new argument `axis.lty', which if set to 1
        allows the pre-1.6.0 behaviour of plotting the axis and tick
        marks for the categorical axis.  (This was apparently not
        intentional, but axis() used to ignore lty=0.)
        The argument `border' is no longer ".NotYetUsed".


                CHANGES IN R VERSION 1.6.0

USER-VISIBLE CHANGES

    o   The default colour palette now has "grey" instead of "white"
        in location 8.  See palette().

    o   grid(nx) behaves differently (but the same as in R versions <= 0.64).

NEW FEATURES

    o   Preparations for name space support:

    o   The objects created in the methods package to represent
        classes, generic functions, method definitions, and
        inheritance relations now themselves belong to true classes.  In
        particular, the "classRepresentation" objects follow the description
        in "Programming with Data" (section 7.6).

    o   Other additions and changes to the methods package:

    o   New methods ([[, print, str) and extended plot() method
        (incl. logical `horiz') for "dendrogram" class.

    o   sprintf() now checks the agreement between formats and object
        types, and handles special values (NA, Inf, ...) correctly.

    o   chol() now uses a tolerance for non-positive-definiteness and
        so should give more consistent results across platforms.

    o   New function agrep() for approximate (fuzzy) string matching.

    o   help.search() can now use both approximate (fuzzy) and regular
        expression matching.  By default, if the pattern to be matched
        consists of only alphanumeric characters, whitespace or a dash,
        approximate matching is used.

    o   axis() has three new optional arguments `col', `lty', and `lwd'
        all for drawing the axis line and tick marks.

    o   Function vcov() (formerly in MASS), a generic function to
        return the variance-covariance matrix of the parameter
        estimates of a fitted model.

    o   duplicated() and unique() have methods for matrices and arrays
        (based on ideas from Jens Oehlschl<E4>gel).

    o   Internally memory sizes and counts of cons cells are now stored
        in unsigned longs.  This allows memory limits to be set and
        objects created in the range 2-4Gb on 32-bit platforms, and
        allows 64-bit platforms to use much larger amounts of memory.

    o   Command-line flags to set memory can now use the suffix `G'
        for gigabytes.  The setting of maximum vsize is now only
        limited by the platform's address space.

    o   All warning and error messages are truncated to a length set
        by options(warning.length=), defaulting to 1000.  (Previously
        most (but not quite all) were truncated at 8192 characters.)

    o   [dpqr]gamma() check for shape parameter > 0.

    o   as.POSIX[cl]t can now convert logical NAs.

    o   All installed packages (even those shipped with R) are
        given a `Built' field in the DESCRIPTION file.

    o   as.data.frame() now coerces logical matrices into logical
        columns (rather than factors).

    o   [[<-.data.frame no longer coerces character replacement values
        to factor.  This is consistent with using $ to replace and
        with S4.

    o   library() attempts to detect improperly installed packages, so
        as from this version an installed package must have a
        DESCRIPTION file and that file must have been stamped with a
        `Built:' line (which was introduced in 1.2.0).  Under
        Unix-alikes, the platform is checked against that used for
        installation.

    o   print.factor() has new arguments `max.levels' (with a smart default)
        and `width'.  print.ordered() is no longer needed.

    o   RNGkind() has an additional option for normal random generators:
        "Inversion".

    o   data.frame() recycles factors and "AsIs" objects as well as
        atomic vectors.

    o   rect() accepts additional graphics parameters through a ...
        argument (in the same way as polygon).

    o   strwidth/strheight() now coerce their first argument in exactly
        the same way text() does, so a wider range of inputs is allowed.

    o   prompt()'s default and data.frame methods have a new 3rd argument
        `name' allowing them to used more easily in scripts and loops.

    o   rgb() has a new `maxColorValue' argument, allowing r,g,b in [0,M],
        particularly in {0:255}, efficiently and non-error-prone.

    o   summaryRprof() provides the functionality of R CMD Rprof in R
        code, though more slowly.

    o   pdf() now uses PDF not R code for clipping, which ensures that
        partially visible text strings are (partially) shown.

    o   Each R session uses a per-session temporary directory which
        is removed at normal termination.  The directory name is given
        by the tempdir() function, and filenames returned by
        tempfile() will be within that directory.

   o   help.start() on Unix now uses a .R subdirectory of the
        per-session temporary directory and not ~/.R.  A side effect
        is that ~/.R is now never deleted by R.

    o   cbind/rbind() used to ignore all zero-length vectors, an
        undocumented quirk for S-compatibility.  This caused problems
        when combining zero-extent matrices and zero-length vectors, and
        now zero-length vectors are ignored unless the result would
        have zero rows/columns.

    o   plot.spec(x) now also works for other x than AR and Pgram results.

    o   New functions La.chol() and La.chol2inv() for Cholesky
        decomposition and inverse of positive definite matrices using
        Lapack.

    o   Changes to the tcltk package

    o   New function axTicks() returning tick mark locations like axis().

    o   grid() has a more sensible default behavior.  Tick axis alignment
        only happens when no numbers of grid cells are specified.  New
        arguments lwd and equilogs; nx/ny = NA for not drawing, see ?grid.

    o   installed.packages() has a new argument `priority'.

    o   termplot() uses factor levels rather than 1,2,3... for x-axis.

    o   The trace() function has been robustified and a new function
        tracingState() added to turn tracing temporarily on and off.

    o   New cophenetic() in "mva" as utility for hierarchical clustering.

    o   p.adjust() has two new methods, 'Hommel' and 'FDR', contributed
        by Gordon Smyth <smyth@wehi.edu.au>.

    o   stars() now has add and plot arguments.

and lots of bug fixes.

BUILDLINK_X11PKG_DIR is no more.

INSTALL_DIRS -> R_INSTALL_DIRS to not conflict with the variable introduced
in bsd.pkg.mk revision 1.1045.  Fixes pkg/18332

find ... -or ... -> find ... -o ... for more portability.

Update R to 1.5.1, switch to buildlink2, change maintainer.

User-Visible Changes

    o XDR support is now guaranteed to be available, so the default
        save format will always be XDR binary files, and it is safe to
        distribute data in that format. (We are unaware of any
        platform that did not support XDR in recent versions of R.)

        gzfile() is guaranteed to be available, so the preferred
        method to distribute sizeable data objects is now via
        save(compress = TRUE).

    o pie() replaces piechart() and defaults to using pastel colours.

    o formatC has new arguments (see below) and formatC(*, d = <dig>)
        is no longer valid and must be written as formatC(*, digits = <dig>).

    o Missingness of character strings is treated much more
        consistently, and the character string "NA" can be used as a
        non-missing value.

    o summary.factor() now uses a stable sort, so the output will
        change where there are ties in the frequencies.


Plus lots of new features and many bug fixes.

Give path for -lblas so modules such as R-KernSmooth can find it when
they try to link it.

Merge from pkgsrc-current to buildlink2 branch.

don't key off of `alpha' to decide to do OSF specific things (-fpe3 flag
to the fortran compiler).  Also mark as not for older netbsd-alpha systems
as this is an IEEE-754 infected program (hi ross!).

Reorder PLIST so pkg_delete works cleanly

Add etc/Makeconf to REPLACE_BUILDLINK.  Fixes pkg/16620

Change MASTER_SITES to use the CRAN list.

Add support for building R extension packages as pkgsrc packages.
Bump PKGREVISION so extension packages can depend on a version of R with
this support.

Discussed with Johnny Lam.

Give all packages which depend on "png" a version bump, and update
all dependencies on packages depending on "png" which contain shared
libraries, all for the (imminent) update to the "png" package.
[List courtesy of John Darrow, courtesy of "bulk-build".]

Update to version 1.4.1 from PR pkg/15757 by Ray Brownrigg with minor mods
by me.

Changes and bug fixes from 1.3.1 are numerous.  See the NEWS file in
the distribution for details.

Include a patch for the generated configure script so that we don't have
to depend on auto* tools at build-time.  This fixes pkg/14916 by Brook
Milligan <brook@biology.nmsu.edu>.

I am a triple idiot.  The only relevant variable that x11.buildlink.mk
redefines about which buildlink.mk files would care is BUILDLINK_X11_DIR,
which points to the location of the X11R6 hierarchy used during building.
If x11.buildlink.mk isn't included, then BUILDLINK_X11_DIR defaults to
${X11BASE} (set in bsd.pkg.mk), so its value is always safe to use.  Remove
the ifdefs surrounding the use of BUILDLINK_X11_DIR in tk/buildlink.mk and
revert changes to move x11.buildlink.mk before the other buildlink.mk files.

Use wildcard dependence on "autoconf" package.

Add back COMMENT definition which got lost.

Update R to 1.3.0.  This is a two-generation upgrade from the previous 1.1.1
version in pkgsrc.  There are many, many bugfixes, better compliance with
S3/S4, and many additional statistical analysis functions added to the
base library.  There is also an improved (faster) garbage collector and
support for dynamically sizing the memory used by R.  The full summary of
changes may be found on the R Project website.

LIBS is automatically added to CONFIGURE_ENV by bsd.pkg.mk if
GNU_CONFIGURE is defined, so simply set LIBS to the appropriate value.

CPPFLAGS is now passed to MAKE_ENV and CONFIGURE_ENV by bsd.pkg.mk, so
adapt by moving CPPFLAGS settings to top-level, and removing explicit
inclusion of CPPFLAGS into MAKE_ENV and CONFIGURE_ENV.

Update dependency on png to >=1.0.11 because of the shlib major bump.
Noted by Frederick Bruckman.

Change BUILD_DEPENDS semantics:
first component is now a package name+version/pattern, no more
executable/patchname/whatnot.

While there, introduce BUILD_USES_MSGFMT as shorthand to pull in
devel/gettext unless /usr/bin/msgfmt exists (i.e. on post-1.5 -current).

Patch by Alistair Crooks <agc@netbsd.org>

Because the minor number of the PNG library was increased packages compiled
using the newest PNG library won't work on system with an older one. To
prevent such problems with precompiled binary packages require at least
"png-1.0.9nb1" in all dependences.

Add NOT_FOR_PLATFORMS=*-*-alpha as R requires IEEE math.  Information
gleaned from port-alpha mailing list posting by Paul Mather
<paul@gromit.dlib.vt.edu> in:

	http://mail-index.netbsd.org/port-alpha/2001/02/14/0004.html

Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT.

Make that "autoreconf" -- there is no "autoremake".

Use full pathname "${LOCALBASE}/bin/auto..." in dependences and make
targets. This includes a fix for PR pkg/12125 by Tomasz Luchowski.

Homepage has moved.

Update R to 1.1.1.  This is primarily a bugfix release from version 1.1.0,
particularly fixing the table editor, but also contains a few additions:

    o	data(), example() and help() now search the loaded packages, then
	in their .lib.loc argument, the latter as pre-0.99.0.  See
	their help pages for the precise details.

    o	help() has a new argument `try.all.packages' set by the option
	"help.try.all.packages". If help is not found in the normal
	path and this is TRUE then a search is made of all packages
	for possible matches.

    o   prop.trend.test() - test for trend in proportions.

    o   write.table() has new argument `dec' for setting the decimal
        separator (SPSS/Windows and probably others want commas in
	continental European locales).

    o   Advance warning: save(, oldstyle=TRUE) will no longer be
	available after this release.

    o   Symbols can now be coerced to expressions, making
	as.expression(quote(a)) work

Update R to 1.1.0.  Many additions and bug-fixes from 1.1.0 make this
a more usable replacement for S/S-PLUS.

Update to R-1.0.1.  Move R library tree to ${PREFIX}/lib (a la perl5)
since it contains loadable shared object files that are platform-specific.
Lots of bug-fixes and additions ... it's getting closer to a usable
replacement for S-PLUS.

Update R to 0.90.1.  Changes are tons of changes and bugfixes, too
numerous to list here (see http://cran.r-project.org/src/base/NEWS for
more information).

add USE_FORTRAN

Update R to 0.64.2.  Changes from 0.64.1:

NEW FEATURES

    o   new target for R installation testing :  make strict-tests.

    o   symnum(x) now nicely codes logical x.

    o   convolve() has a new type = c("circular", "open", "filter")
        argument allowing more than the only circular convolution.

    o   par(xpd) now has three settings:  FALSE (clip to plot region),
        TRUE (clip to figure region), or NA (clip to device region).

    o   zapsmall(x) works for complex x.

    o   new global variable R.version.string (for plots & reports).
        Deprecated version & Version for new  R.version & R.Version.

    o   R CMD Rd2dvi  has builtin "Usage" help and works for multiple files.
        Useful for automatic reference manual of a package.
        (doc/manual/lib2tex is more efficient for installed packages, however).

BUG FIXES

    o   power() is now fully implemented and documented.

    o   A couple of problems with group generic operations.

    o   A bug which meant that it was not possible to add elements
        to zero length lists in the obvious way has been fixed.
                x <- list(); x[[1]] <- 10
                x <- list(); x[["a"]] <- 11
        both now work.

    o   save.image() ignored dot-names. (esp. .First())

    o   lab= argument to plot() misinterpreted by axis() via ... passing

    o   NULL labels in text() caused segfault

    o   matrix(f,...) with f a factor now coerces to character

    o   documentation errors for substitute and is.vector, minor fixups for
        trig and nlm

    o   Background colours are set properly on X11 devices with
        colortype="pseudo": sometimes they were not allocated separately.

    o   C() works (again?) for a single argument.

    o   is.na() didn't work properly for "list" arguments.

    o   symnum() sometimes failed with arrays of rank >= 3.

    o   in some cases one could get nonblack color instead of
        black on 2nd x11() window.

    o   influence.measures(.) $ is.influential was wrong on the
        cooks.distance.

    o   printing of complex NaN/Inf was wrong as well.

    o   printing of complex named vectors had a wrong initial space.

    o   allow trailing space in character->numeric coercion

    o   library() gave wrong "masked" warnings in some cases.

    o   par(xpd) semantics were not compatible with S.

    o   rect() output was not clipped in PostScript.

    o   par(pin=c(width, height)) was behaving as par(pin=c(width, width)).

    o   Non-blank separated data files didn't have their 1st field
        handled properly.

    o   "aux" directory moved to "tools" to avoid difficulties on
        Windows.

    o   structure() clobbered factors with missing levels.

    o   pmatch() misbehaved on duplicate matches.

    o   R CMD Rd2dvi <file.Rd> works again.

    o   logical binops tried to set time series parameters before dimensions.

    o   upped the BUFSIZE in model.c (NOT proper long-term solution).

    o   dput(), dump() and deparse()  now always use DBL_DIG (=15) digits
        for numeric formatting.

    o   chull() now works for vertical borders, such as in chull(c(1,1,2),3:1).

Update readline dependency.

default R_PAPERSIZE to A4 if PAPERSIZE is not set.

Updated R to 0.64.1.  Too many changes from 0.62.1 to enumerate.
See NEWS file in distribution.

add USE_X11=yes

Fix CONFLICTS (remove redundancy, mostly)

Reflect update of f2c.

Update R to 0.63.1, provided in pr 6618 by Johnny C. Lam.

Changes since 0.63.0 are mostly bigfixes and patches that make it
actually work properly with NetBSD.

Initial addition of R-0.63.0, a language for data analysis and graphics.
Provided in pr 6493 by Johnny C. Lam.

Initial revision