Log message:
Don't pass -I without argument to the compiler.

Log message:
Remove pkgviews: don't set PKG_INSTALLATION_TYPES in Makefiles.

Log message:
Replace WRAPPER_BINDIR reference with real path in generated file.

Log message:
Update R to 3.1.1

NEW FEATURES:

    * When attach() reports conflicts, it does so compatibly with
      library() by using message().

    * R CMD Sweave no longer cleans any files by default, compatibly
      with versions of R prior to 3.1.0.  There are new options
      --clean, --clean=default and --clean=keepOuts.

    * tools::buildVignette() and tools::buildVignettes() with clean =
      FALSE no longer remove any created files.  buildvignette() gains
      a keep argument for more cleaning customization.

    * The Bioconductor 'version' used by setRepositories() can now be
      set by environment variable R_BIOC_VERSION at runtime, not just
      when R is installed.  (It has been stated that Bioconductor will
      switch from 'version' 2.14 to 'version' 3.0 during the lifetime
      of the R 3.1 series.)

    * Error messages from bugs in embedded Sexpr code in Sweave
      documents now report the source location.

    * type.convert(), read.table() and similar read.*() functions get a
      new numerals argument, specifying how numeric input is converted
      when its conversion to double precision loses accuracy.  The
      default value, "allow.loss" allows accuracy loss, as in R
      versions before 3.1.0.

    * For some compilers, integer addition could overflow without a
      warning.  R's internal code for both integer addition and
      subtraction is more robust now.

    * The function determining the default number of knots for
      smooth.spline() is now exported, as .nknots.smspl().

    * dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
      for a = 0, b = 0, or infinite a and b (where they typically
      returned NaN before).

    * Many package authors report that the RStudio graphics device does
      not work correctly with their package's use of dev.new().  The
      new option dev.new(noRStudioGD = TRUE) replaces the RStudio
      override by the default device as selected by R itself, still
      respecting environment variables R_INTERACTIVE_DEVICE and
      R_DEFAULT_DEVICE.

    * readRDS() now returns visibly.

    * Modifying internal logical scalar constants now results in an
      error instead of a warning.

    * install.packages(repos = NULL) now accepts http:// or ftp:// URLs
      of package archives as well as file paths, and will download as
      required.  In most cases repos = NULL can be deduced from the
      extension of the URL.

    * The warning when using partial matching with the $ operator on
      data frames is now only given when
      options("warnPartialMatchDollar") is TRUE.

    * Package help requests like package?foo now try the package foo
      whether loaded or not.

    * General help requests now default to trying all loaded packages,
      not just those on the search path.

    * Added a new function promptImport(), to generate a help page for
      a function that was imported from another package (and presumably
      re-exported, or help would not be needed).

Log message:
FreeBSD 10 is not FreeBSD 1.

Log message:
Bump for perl-5.20.0.
Do it for all packages that
* mention perl, or
* have a directory name starting with p5-*, or
* depend on a package starting with p5-
like last time, for 5.18, where this didn't lead to complaints.
Let me know if you have any this time.

Log message:
Recursive revbump from x11/pixman
Fix PR pkg/48777

Log message:
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().

Log message:
Update to R 3.0.3.   update from wen heping.

CHANGES IN R 3.0.3:

NEW FEATURES:

* On Windows there is support for making .texi manuals using
  texinfo 5.0 or later: the setting is in file
  src/gnuwin32/MkRules.dist.

  A packaging of the Perl script and modules for texinfo 5.2 has
  been made available at <URL:
  http://www.stats.ox.ac.uk/pub/Rtools/>.

* write.table() now handles matrices of 2^31 or more elements, for
  those with large amounts of patience and disc space.

* There is a new function, La_version(), to report the version of
  LAPACK in use.

* The HTML version of 'An Introduction to R' now has links to PNG
  versions of the figures.

* There is some support to produce manuals in ebook formats. (See
  doc/manual/Makefile.  Suggested by Mauro Cavalcanti.)

* On a Unix-alike Sys.timezone() returns NA if the environment
  variable TZ is unset, to distinguish it from an empty string
  which on some OSes means the UTC time zone.

* The backtick may now be escaped in strings, to allow names
  containing them to be constructed, e.g. `\``.

* read.table(), readLines() and scan() now warn when an embedded
  nul is found in the input.

* KalmanForecast(fast = FALSE) is now the default, and the help
  contains an example of how fast = TRUE can be used in this
  version.  (The usage will change in 3.1.0.)

* strptime() now checks the locale only when locale-specific
  formats are used and caches the locale in use: this can halve the
  time taken on OSes with slow system functions (e.g. OS X).

* strptime() and the format() methods for classes "POSIXct",
  "POSIXlt" and "Date" recognize strings with marked encodings:
  this allows, for example, UTF-8 French month names to be read on
  (French) Windows.

* iconv(to = "utf8") is now accepted on all platforms (some
  implementations did already, but GNU libiconv did not: however
  converted strings were not marked as being in UTF-8).  The
  official name, "UTF-8" is still preferred.

* available.packages() is better protected against corrupt metadata
  files.

* Finalizers are marked to be run at garbage collection, but run
  only at a somewhat safer later time (when interrupts are
  checked).  This circumvents some problems with finalizers running
  arbitrary code during garbage collection (the known instances
  being running options() and (C-level) path.expand()
  re-entrantly).

Log message:
Set USE_GCC_RUNTIME=yes for packages which build shared libraries but do
not use libtool to do so.  This is required to correctly depend upon a
gcc runtime package (e.g. gcc47-libs) when using USE_PKGSRC_GCC_RUNTIME.