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Date: Wed, 13 May 2015 12:48:06 +0000
From: "Ryo ONODERA" <ryoon@netbsd.org>
Subject: CVS commit: pkgsrc/math/R
To: pkgsrc-changes@NetBSD.org
Reply-To: ryoon@netbsd.org
Message-Id: <20150513124806.106CB98@cvs.netbsd.org>
Sender: pkgsrc-changes-owner@NetBSD.org
Precedence: bulk

Module Name:	pkgsrc
Committed By:	ryoon
Date:		Wed May 13 12:48:06 UTC 2015

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

Log Message:
Update to 3.2.0

Changelog:
CHANGES IN 3.2.0:

  NEW FEATURES:

    * anyNA() gains a recursive argument.

    * When x is missing and names is not false (including the default
      value), Sys.getenv(x, names) returns an object of class "Dlist"
      and hence prints tidily.

    * (Windows.)  shell() no longer consults the environment variable
      SHELL: too many systems have been encountered where it was set
      incorrectly (usually to a path where software was compiled, not
      where it was installed).  R_SHELL, the preferred way to select a
      non-default shell, can be used instead.

    * Some unusual arguments to embedFonts() can now be specified as
      character vectors, and the defaults have been changed
      accordingly.

    * Functions in the Summary group duplicate less.  (PR#15798)

    * (Unix-alikes.) system(cmd, input = ) now uses
      'shell-execution-environment' redirection, which will be more
      natural if cmd is not a single command (but requires a
      POSIX-compliant shell). (Wish of PR#15508)

    * read.fwf() and read.DIF() gain a fileEncoding argument, for
      convenience.

    * Graphics devices can add attributes to their description in
      .Device and .Devices.  Several of those included with R use a
      "filepath" attribute.

    * pmatch() uses hashing in more cases and so is faster at the
      expense of using more memory. (PR#15697)

    * pairs() gains new arguments to select sets of variables to be
      plotted against each other.

    * file.info(, extra_cols = FALSE) allows a minimal set of columns
      to be computed on Unix-alikes: on some systems without
      properly-configured caching this can be significantly faster with
      large file lists.

    * New function dir.exists() in package base to test efficiently
      whether one or more paths exist and are directories.

    * dput() and friends gain new controls hexNumeric and digits17
      which output double and complex quantities as, respectively,
      binary fractions (exactly, see sprintf("%a")) and as decimals
      with up to 17 significant digits.

    * save(), saveRDS() and serialize() now support ascii = NA which
      writes ASCII files using sprintf("%a") for double/complex
      quantities.  This is read-compatible with ascii = TRUE but avoids
      binary->decimal->binary conversions with potential loss of
      precision.  Unfortunately the Windows C runtime's lack of C99
      compliance means that the format cannot be read correctly there
      in R before 3.1.2.

    * The default for formatC(decimal.mark =) has been changed to be
      getOption("OutDec"); this makes it more consistent with format()
      and suitable for use in print methods, e.g. those for classes
      "density", "ecdf", "stepfun" and "summary.lm".

      getOption("OutDec") is now consulted by the print method for
      class "kmeans", by cut(), dendrogram(), plot.ts() and quantile()
      when constructing labels and for the report from legend(trace =
      TRUE).

      (In part, wish of PR#15819.)

    * printNum() and hence format() and formatC() give a warning if
      big.mark and decimal.mark are set to the same value (period and
      comma are not uncommonly used for each, and this is a check that
      conventions have not got mixed).

    * merge() can create a result which uses long vectors on 64-bit
      platforms.

    * dget() gains a new argument keep.source which defaults to FALSE
      for speed (dput() and dget() are most often used for data objects
      where this can make dget() many times faster).

    * Packages may now use a file of common macro definitions in their
      help files, and may import definitions from other packages.

    * A number of macros have been added in the new share/Rd directory
      for use in package overview help pages, and promptPackage() now
      makes use of them.

    * tools::parse_Rd() gains a new permissive argument which converts
      unrecognized macros into text.  This is used by
      utils:::format.bibentry to allow LaTeX markup to be ignored.

    * options(OutDec =) can now specify a multi-byte character, e.g.,
      options(OutDec = "\u00b7") in a UTF-8 locale.

    * is.recursive(x) is no longer true when x is an external pointer,
      a weak reference or byte code; the first enables all.equal(x, x)
      when x <- getClass(.).

    * ls() (aka objects()) and as.list.environment() gain a new
      argument sorted.

    * The "source" attribute (which has not been added to functions by
      R since before R version 2.14.0) is no longer treated as special.

    * Function returnValue() has been added to give on.exit() code
      access to a function's return value for debugging purposes.

    * crossprod(x, y) allows more matrix coercions when x or y are
      vectors, now equalling t(x) %*% y in these cases (also reported
      by Radford Neal).  Similarly, tcrossprod(x,y) and %*% work in
      more cases with vector arguments.

    * Utility function dynGet() useful for detecting cycles, aka
      infinite recursions.

    * The byte-code compiler and interpreter include new instructions
      that allow many scalar subsetting and assignment and scalar
      arithmetic operations to be handled more efficiently. This can
      result in significant performance improvements in scalar
      numerical code.

    * apply(m, 2, identity) is now the same as the matrix m when it has
      _named_ row names.

    * A new function debuggingState() has been added, allowing to
      temporarily turn off debugging.

    * example() gets a new optional argument run.donttest and
      tools::Rd2ex() a corresponding commentDonttest, with a default
      such that example(..) in help examples will run \donttest code
      only if used interactively (a change in behaviour).

    * rbind.data.frame() gains an optional argument make.row.names, for
      potential speedup.

    * New function extSoftVersion() to report on the versions of
      third-party software in use in this session.  Currently reports
      versions of zlib, bzlib, the liblzma from xz, PCRE, ICU, TRE and
      the iconv implementation.

      A similar function grSoftVersion() in package grDevices reports
      on third-party graphics software.

      Function tcltk::tclVersion() reports the Tcl/Tk version.

    * Calling callGeneric() without arguments now works with primitive
      generics to some extent.

    * vapply(x, FUN, FUN.VALUE) is more efficient notably for large
      length(FUN.VALUE); as extension of PR#16061.

    * as.table() now allows tables with one or more dimensions of
      length 0 (such as as.table(integer())).

    * names(x) <- NULL now clears the names of call and ... objects.

    * library() will report a warning when an insufficient dependency
      version is masking a sufficient one later on the library search
      path.

    * A new plot() method for class "raster" has been added.

    * New check_packages_in_dir_changes() function in package tools for
      conveniently analyzing how changing sources impacts the check
      results of their reverse dependencies.

    * Speed-up from Peter Haverty for ls() and
      methods:::.requirePackage() speeding up package loading.
      (PR#16133)

    * New get0() function, combining exists() and get() in one call,
      for efficiency.

    * match.call() gains an envir argument for specifying the
      environment from which to retrieve the ... in the call, if any;
      this environment was wrong (or at least undesirable) when the
      definition argument was a function.

    * topenv() has been made .Internal() for speedup, based on Peter
      Haverty's proposal in PR#16140.

    * getOption() no longer calls options() in the main case.

    * Optional use of libcurl (version 7.28.0 from Oct 2012 or later)
      for Internet access:

        * capabilities("libcurl") reports if this is available.

        * libcurlVersion() reports the version in use, and other
          details of the "libcurl" build including which URL schemes it
          supports.

        * curlGetHeaders() retrieves the headers for http://, https://,
          ftp:// and ftps:// URLs: analysis of these headers can
          provide insights into the `existence' of a URL (it might for
          example be permanently redirected) and is so used in R CMD
          check --as-cran.

        * download.file() has a new optional method "libcurl" which
          will handle more URL schemes, follow redirections, and allows
          simultaneous downloads of multiple URLs.

        * url() has a new method "libcurl" which handles more URL
          schemes and follows redirections.  The default method is
          controlled by a new option url.method, which applies also to
          the opening of URLs _via_ file() (which happens implicitly in
          functions such as read.table.)

        * When file() or url() is invoked with a https:// or ftps://
          URL which the current method cannot handle, it switches to a
          suitable method if one is available.

    * (Windows.) The DLLs internet.dll and internet2.dll have been
      merged.  In this version it is safe to switch (repeatedly)
      between the internal and Windows internet functions within an R
      session.

      The Windows internet functions are still selected by flag
      --internet2 or setInternet2().  This can be overridden for an
      url() connection _via_ its new method argument.

      download.file() has new method "wininet", selected as the default
      by --internet2 or setInternet2().

    * parent.env<- can no longer modify the parent of a locked
      namespace or namespace imports environment.  Contributed by Karl
      Millar.

    * New function isLoadedNamespace() for readability and speed.

    * names(env) now returns all the object names of an environment
      env, equivalently to ls(env, all.names = TRUE, sorted = FALSE)
      and also to the names of the corresponding list,
      names(as.list(env, all.names = TRUE)).  Note that although
      names() returns a character vector, the names have no particular
      ordering.

    * The memory manager now grows the heap more aggressively. This
      reduces the number of garbage collections, in particular while
      data or code are loaded, at the expense of slightly increasing
      the memory footprint.

    * New function trimws() for removing leading/trailing whitespace.

    * cbind() and rbind() now consider S4 inheritance during S3
      dispatch and also obey deparse.level.

    * cbind() and rbind() will delegate recursively to methods::cbind2
      (methods::rbind2) when at least one argument is an S4 object and
      S3 dispatch fails (due to ambiguity).

    * (Windows.)  download.file(quiet = FALSE) now uses text rather
      than Windows progress bars in non-interactive use.

    * New function hsearch_db() in package utils for building and
      retrieving the help search database used by help.search(), along
      with functions for inspecting the concepts and keywords in the
      help search database.

    * New function .getNamespaceInfo(), a no-check version of
      getNamespaceInfo() mostly for internal speedups.

    * The help search system now takes \keyword entries in Rd files
      which are not standard keywords (as given in KEYWORDS in the R
      documentation directory) as concepts.  For standard keyword
      entries the corresponding descriptions are additionally taken as
      concepts.

    * New lengths() function for getting the lengths of all elements in
      a list.

    * New function toTitleCase() in package tools, tailored to package
      titles.

    * The matrix methods of cbind() and rbind() allow matrices as
      inputs which have 2^31 or more elements.  (For cbind(), wish of
      PR#16198.)

    * The default method of image() has an explicit check for a numeric
      or logical matrix (which was always required).

    * URLencode() will not by default encode further URLs which appear
      to be already encoded.

    * BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima()
      fitted models, as nobs(mod) now gives the number of "used"
      observations for such models.  This fixes PR#16198, quite
      differently than proposed there.

    * The print() methods for "htest", "pairwise.htest" and
      "power.htest" objects now have a digits argument defaulting to (a
      function of) getOption("digits"), and influencing all printed
      numbers coherently.  Unavoidably, this changes the display of
      such test results in some cases.

    * Code completion for namespaces now recognizes all loaded
      namespaces, rather than only the ones that are also attached.

    * The code completion mechanism can now be replaced by a
      user-specified completer function, for (temporary) situations
      where the usual code completion is inappropriate.

    * unzip() will now warn if it is able to detect truncation when
      unpacking a file of 4GB or more (related to PR#16243).

    * methods() reports S4 in addition to S3 methods; output is
      simplified when the class argument is used.  .S3methods() and
      methods::.S4methods() report S3 and S4 methods separately.

    * Higher order functions such as the apply functions and Reduce()
      now force arguments to the functions they apply in order to
      eliminate undesirable interactions between lazy evaluation and
      variable capture in closures.  This resolves PR#16093.

  INSTALLATION and INCLUDED SOFTWARE:

    * The \donttest sections of R's help files can be tested by
      make check TEST_DONTTEST=TRUE .

    * It is possible to request the use of system valgrind headers
      _via_ configure option --with-system-valgrind-headers: note the
      possible future incompatibility of such headers discussed in the
      'R Installation and Administration' manual. (Wish of PR#16068.)

    * The included version of liblzma has been updated to xz-utils
      5.0.7 (minor bug fixes from 5.0.5).

    * configure options --with-system-zlib, --with-system-bzlib and
      --with-system-pcre are now the default.  For the time being there
      is fallback to the versions included in the R sources if no
      system versions are found or (unlikely) if they are too old.

      Linux users should check that the -devel or -dev versions of
      packages zlib, bzip2/libbz2 and pcre as well as
      xz-devel/liblzma-dev (or similar names) are installed.

    * configure by default looks for the texi2any script from texinfo
      5.1 or later, rather than the makeinfo program.  (makeinfo is a
      link to the Perl script texi2any in texinfo 5.x.)

    * R CMD INSTALL gains an option --built-timestamp=STAMP allowing
      100% reproducible package building, thanks to Dirk Eddelbuettel.

  UTILITIES:

    * There is support for testing the \dontrun and \donttest parts of
      examples in packages.

      tools::testInstalledPackage() accepts new arguments
      commentDontrun = FALSE and commentDonttest = FALSE.

      R CMD check gains options --run-dontrun and --run-donttest.

    * The HTML generated by tools::Rd2HTML() and tools::toHTML()
      methods is now 'XHTML 1.0 Strict'.

    * The compiler package's utility function setCompilerOptions() now
      returns the old values invisibly. The initial optimization level
      can also be set with the environment variable
      R_COMPILER_OPTIMIZE.

    * R CMD build adds a NeedsCompilation field if one is not already
      present in the DESCRIPTION file.

    * R CMD check gains option --test-dir to specify an alternative set
      of tests to run.

    * R CMD check will now by default continue with testing after many
      types of errors, and will output a summary count of errors at the
      end if any have occurred.

    * R CMD check now checks that the Title and Description fields are
      correctly terminated.

    * R CMD check --as-cran now:

        * checks a README.md file can be processed: this needs pandoc
          installed.

        * checks the existence and accessibility of URLs in the
          DESCRIPTION, CITATION, NEWS.Rd and README.md files and in the
          help files (provided the build has libcurl support).

        * reports non-ASCII characters in R source files when there is
          no package encoding declared in the DESCRIPTION file.

        * reports (apparent) S3 methods exported but not registered.

        * reports overwriting registered S3 methods from
          base/recommended packages.  (Such methods are replaced in the
          affected package for the rest of the session, even if the
          replacing namespace is unloaded.)

        * reports if the Title field does not appear to be in title
          case (see 'Writing R Extensions': there may be false
          positives, but note that technical words should be
          single-quoted and will then be accepted).

      Most of these checks can also be selected by environment
      variables: see the 'R Internals' manual.

  C-LEVEL FACILITIES:

    * New C API utility logspace_sum(logx[], n).

    * Entry points rbinom_mu, rnbinom_mu and rmultinom are remapped (by
      default) to Rf_rbinom_mu etc.  This requires packages using them
      to be re-installed.

    * .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now ignored, so
      arguments are duplicated if DUP = TRUE would do so.  As their
      help has long said, .Call() is much preferred.

    * New entry point R_allocLD, like R_alloc but guaranteed to have
      sufficient alignment for long double pointers.

    * isPairList() now returns TRUE for DOTSXP.

  WINDOWS BUILD CHANGES:

  A number of changes to the Windows build system are in development.
  The following are currently in place.

    * Installation using external binary distributions of zlib, bzip2,
      liblzma, pcre, libpng, jpeglib and libtiff is now required, and
      the build instructions have been revised.

    * A new make target rsync-extsoft has been added to obtain copies
      of the external libraries from CRAN.

    * Building the manuals now requires texi2any from texinfo 5.1 or
      later.  CRAN binary builds include the manuals, but by default
      builds from source will not, and they will be accessed from CRAN.
      See the comments in src/gnuwin32/MkRules.dist for how to specify
      the location of texi2any.

    * (Windows) Changes have been made to support an experimental
      Windows toolchain based on GCC 4.9.2.  The default toolchain
      continues to be based on GCC 4.6.3, as the new toolchain is not
      yet stable enough.  A change to a new toolchain is expected
      during the R 3.2.x lifetime.

  PACKAGE INSTALLATION:

    * (Windows) The use of macro ZLIB_LIBS in file src/Makevars.win
      (which has not been documented for a long time) now requires an
      external libz.a to be available (it is part of the 'goodies' used
      to compile Windows binary packages).  It would be simpler to use
      -lz instead.

    * The default for option pkgType on platforms using binary packages
      is now "both", so source packages will be tried if binary
      versions are not available or not up to date.

      There are options for what install.packages(type = "both")
      (possibly called _via_ update.packages()) will do if compilation
      of a source package is desirable: see ?options (under utils).

      If you intend not to accept updates as source packages, you
      should use update.packages(type = "binary").

  DEPRECATED AND DEFUNCT:

    * download.file(method = "lynx") is defunct.

    * Building R using the included versions of zlib, bzip2, xz and
      PCRE is deprecated: these are frozen (bar essential bug-fixes)
      and will be removed for R 3.3.0.

    * The configure option --with-valgrind-instrumentation=3 has been
      withdrawn, as it did not work with recent valgrind headers: it is
      now treated as level 2.

    * The MethodsList class in package methods had been deprecated in R
      2.11.0 and is defunct now.  Functions using it are defunct if
      they had been deprecated in R 2.11.0, and are deprecated now,
      otherwise.

  BUG FIXES:

    * Fixed two obscure bugs in pairlist subassignment, reported by
      Radford Neal as part of pqR issue 16.

    * Fixes for bugs in handling empty arguments and argument matching
      by name in log().

    * all.equal() gains methods for environments and refClasses.

    * [<- and [[<- gain S4 data.frame methods to avoid corruption of S4
      class information by the S3 methods.

    * callNextMethod() should now work within a .local call when ... is
      absent from formals(.local).

    * dput(pairlist(x)) generates a call to the pairlist constructor
      instead of the list constructor.

    * Fix missing() when arguments are propagated through ... .
      (PR#15707)

    * eigen(m) now defaults to symmetric = TRUE even when the dimnames
      are asymmetric if the matrix is otherwise symmetric.  (PR#16151)

    * Fix issues with forwarding ... through callGeneric() and
      callNextMethod().  (PR#16141)

    * callGeneric() now works after a callNextMethod().

    * Subclass information is kept consistent when replacing an
      ordinary S4 class with an "old class" _via_ the S4Class argument
      to setOldClass(). Thus, for example, a data.frame is valid for a
      list argument in the signature, and a factor is valid for vector
      arguments.

    * In qbeta() the inversion of pbeta() is much more sophisticated.
      This works better in corner cases some of which failed completely
      previously (PR#15755), or were using too many iterations.

    * Auto-printing no longer duplicates objects when printing is
      dispatched to a method.

    * kmeans(x, k) would fail when nrow(x) >= 42949673.  (Comment 6 of
      PR#15364)

    * 'Abbreviated' locale-specific day and month names could have been
      truncated in those rare locales where there are the same as the
      full names.

    * An irrelevant warning message from updating subclass information
      was silenced (the namespace would not be writable in this case).

CHANGES IN R 3.1.3:

  NEW FEATURES:

    * The internal method of download.file() can now handle files
      larger than 2GB on 32-bit builds which support such files (tested
      on 32-bit R running on 64-bit Windows).

    * kruskal.test() warns on more types of suspicious input.

    * The as.dendrogram() method for "hclust" objects gains a check
      argument protecting against memory explosion for invalid inputs.

    * capabilities() has a new item long.double which indicates if the
      build uses a long double type which is longer than double.

    * nlm() no longer modifies the callback argument in place (a new
      vector is allocated for each invocation, which mimics the
      implicit duplication that occurred in R < 3.1.0); note that this
      is a change from the previously documented behavior. (PR#15958)

    * icuSetCollate() now accepts locale = "ASCII" which uses the basic
      C function strcmp and so collates strings byte-by-byte in
      numerical order.

    * sessionInfo() tries to report the OS version in use (not just
      that compiled under, and including details of Linux
      distributions).

    * model.frame() (used by lm() and many other modelling functions)
      now warns when it drops contrasts from factors.  (Wish of
      PR#16119)

    * install.packages() and friends now accept the value type =
      "binary" as a synonym for the native binary type on the platform
      (if it has one).

    * Single source or binary files can be supplied for
      install.packages(type = "both") and the appropriate type and
      repos = NULL will be inferred.

    * New function pcre_config() to report on some of the configuration
      options of the version of PCRE in use.  In particular, this
      reports if regular expressions using \p{xx} are supported.

    * (Windows.) download.file(cacheOK = FALSE) is now supported when
      internet2.dll is used.

    * browseURL() has been updated to work with Firefox 36.0 which has
      dropped support for the -remote interface.

  INSTALLATION and INCLUDED SOFTWARE:

    * The included version of PCRE has been updated to 8.36.

    * configure accepts MAKEINFO=texi2any as another way to ensure
      texinfo 5.x is used when both 5.x and 4.x are installed.

  UTILITIES:

    * R CMD check now checks the packages used in \donttest sections of
      the examples are specified in the DESCRIPTION file.  (These are
      needed to run the examples interactively.)

    * R CMD check checks for the undeclared use of GNU extensions in
      Makefiles, and for Makefiles with a missing final linefeed.

      R CMD build will correct line endings in all Makefiles, not just
      those in the src directory.

    * R CMD check notes uses of library() and require() in package
      code: see the section 'Suggested packages' of 'Writing R
      Extensions' for good practice.

  DEPRECATED AND DEFUNCT:

    * The configure option --with-valgrind-instrumentation=3 is
      deprecated and will be removed in R 3.2.0.

  BUG FIXES:

    * (Windows.) Rscript.exe was missing a manifest specifying the
      modern style for common controls (e.g., the download progress
      bar).

    * If a package had extra documentation files but no vignette, the
      HTML help system produced an empty index page.

    * The parser now gives an error if a null character is included in
      a string using Unicode escapes. (PR#16046)

    * qr.Q() failed on complex arguments due to pre-3.0(!) typo.
      (PR#16054)

    * abs() failed with named arguments when the argument was complex.
      (PR#16047)

    * "noquote" objects may now be used as columns in dataframes.
      (PR#15997)

    * Some values with extremely long names were printed incorrectly.
      (PR#15999)

    * Extremely large exponents on zero expressed in scientific
      notation (e.g. 0.0e50000) could give NaN.  (PR#15976)

    * download.file() reported downloaded sizes as 0KB if less than
      1MB, only for R 3.1.2 and only on big-endian platforms.

    * prompt() did not escape percent signs in the automatically
      generated usage section of help files.

    * drop.terms() dropped some of the attributes of the object it was
      working with.  (PR#16029)

    * (Windows.) The command completion in Rgui.exe messed up the
      console.  (PR#15791)

    * (Windows.) The choose.files() command returned a blank string
      when the user asked for a single file but cancelled the request.
      (PR#16074)

    * Math2 S4 group generics failed to correctly dispatch "structure"-
      and "nonStructure"-derived classes.

    * loadNamespace() imposed undocumented restrictions on the
      versionCheck parameter.  (Reported by Geoff Lee.)

    * Rare over-runs detected by AddressSanitizer in substr() and its
      replacement version have been avoided.

      _Inter alia_ that fix gives the documented behaviour for
      substr(x, 1, 2) <- "" (subsequently reported as PR#16214).

    * Loading packages incorrectly defining an S4 generic followed by a
      function of the same name caused an erroneous cyclic namespace
      dependency error.

    * Declared vignette encodings are now always passed to the vignette
      engine.

    * Port Tomas Kalibera's fix from R-devel that restores the
      loadMethod() fast path, effectively doubling the speed of S4
      dispatch.

    * power.t.test() and power.prop.test() now make use of the
      extendInt option of uniroot() and hence work in more extreme
      cases.  (PR#15792)

    * If a package was updated and attached when its namespace was
      already loaded, it could end up with parts from one version and
      parts from the other.  (PR#16120)

    * tools:::.Rdconv() didn't accept --encoding= due to a typo.
      (PR#16121)

    * Unix-alike builds without a suitable makeinfo were documented to
      link the missing HTML manuals to CRAN, but did not.

    * save(*, ascii=TRUE) and load() now correctly deal with NaN's.
      (PR#16137)

    * split.Date() retains fractional representations while avoiding
      incomplete class propagation.

    * R_ext/Lapack.h had not been updated for changes made by LAPACK to
      the argument lists of its (largely internal) functions dlaed2 and
      dlaed3.  (PR#16157)

    * RShowDoc("NEWS", "txt") had not been updated for the layout
      changes of R 3.1.0.

    * The xtfrm() method for class "Surv" has been corrected and its
      description expanded.

    * mode(x) <- y would incorrectly evaluate x before changing its
      mode. (PR#16215)

    * besselJ(1, 2^64) and besselY(..) now signal a warning, returning
      NaN instead of typically segfaulting. (Issue 3 of PR#15554)

    * HTML conversion of \href markup in .Rd files did not remove the
      backslash from \% and so gave an invalid URL.  In a related
      change, the \ escape is now required in such URLs.

CHANGES IN R 3.1.2:

  NEW FEATURES:

    * embedFonts() now defaults to format = "ps2write" for .ps and .eps
      files.  This is available in Ghostscript 9.x (since 2010) whereas
      the previous default, format = "pswrite", was removed in
      Ghostscript 9.10.

    * For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
      point mass at exp(mulog) rather than return NaN (for an error).

    * capabilities() now reports if ICU is compiled in for use for
      collation (it is only actually used if a suitable locale is set
      for collation, and never for a C locale).

    * (OS X only.) Package tcltk checks when loaded if it is linked
      against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
      component and the X11 libraries are installed.  This allows more
      informative error messages to be given advising the installation
      of the missing component or of XQuartz.

      The X11() device and X11-based versions of the data editor and
      viewer (invoked by edit() and View() for data frames and matrices
      from command-line R) check that the X11 libraries are installed
      and if not advises installing XQuartz.

    * icuSetCollate() allows locale = "default", and locale = "none" to
      use OS services rather than ICU for collation.

      Environment variable R_ICU_LOCALE can be used to set the default
      ICU locale, in case the one derived from the OS locale is
      inappropriate (this is currently necessary on Windows).

    * New function icuGetCollate() to report on the ICU collation
      locale in use (if any).

    * utils::URLencode() was updated to use unreserved and reserved
      characters from RFC 3986 (<URL:
      http://tools.ietf.org/html/rfc3986>) instead of RFC 1738.

    * unique(warnings()) and c(warnings()) are now supported.

    * The Bioconductor 'version' used by setRepositories() now defaults
      to 3.0. (It can be set at runtime _via_ environment variable
      R_BIOC_VERSION.)

    * Omegahat is no longer listed as providing Windows binary
      packages, e.g. by setRepositories().  It has no binary packages
      available for R 3.1.x and those for earlier versions were 32-bit
      only.

  INSTALLATION and INCLUDED SOFTWARE:

    * The configure script reports on the more important
      capabilities/options which will not be compiled in.

      More types of external BLAS are recognized by name in that
      report.

    * When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
      flag is placed earlier in the link commands used during
      installation and when packages are installed: this helps ensure
      that the current build has priority if an R shared library has
      already been installed by e.g. install-libR in a library
      mentioned in LDFLAGS (and not in 'your system's library
      directory' as documented). (Wish of PR#15790.)

    * LaTeX package upquote is no longer required for R's use of
      inconsolata.

    * (Windows only) If both 32- and 64-bit versions of R are
      installed, the bin/R.exe and bin/Rscript.exe executables now run
      64-bit R.  (To run 32-bit R, overwrite these files with copies of
      bin/i386/Rfe.exe.)

  UTILITIES:

    * Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
      the VignetteBuilder packages available even if they are listed in
      Suggests, since they are needed to recognise and process
      non-Sweave vignettes.

    * R CMD check now reports empty importFrom declarations in a
      NAMESPACE file, as these are common errors (writing
      importFrom(Pkg) where import(Pkg) was intended).

    * R CMD check now by default checks code usage directly on the
      package namespace without loading and attaching the package and
      its suggests and enhances.  For good practice with packages in
      the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'.  For
      use of lazy-data objects in the package's own code, see ?data.

  BUG FIXES:

    * dmultinom() did not handle non-finite probabilities correctly.

    * prettyNum(x, zero.print=*) now also works when x contains NAs.

    * A longstanding bug exhibited by nlminb() on Windows was traced to
      a compiler bug in gcc 4.6.3; a workaround has been put in place.
      (PR#15244 and PR#15914).

    * Rendering of \command in HTML versions of help pages has been
      improved: this is particularly evident on the help page for
      INSTALL.

    * as.hexmode(x) and as.octmode(x) now behave correctly for some
      numeric x, e.g., c(NA, 1) or c(1, pi).

    * drop1() failed if the scope argument had no variables to drop.
      (PR#15935)

    * edit() (and hence fix()) failed if an object had a non-character
      attribute named "source" (an attribute that had been used in R
      prior to version 2.14.0).

    * callGeneric() could fail if the generic had ... as a formal
      argument. (PR#15937).

    * Forking in package parallel called C entry point exit in the
      child.  This was unsafe (_exit should have been called), and
      could flush stdin of the main R process (seen most often on
      Solaris).

      As good practice, stdout is now flushed before forking a child.

    * R objects such as list(`a\b` = 1) now print correctly.

    * getAnywhere("C_pbinom") now returns correctly a single object
      (rather than unlisting it).

    * The confint() method for nls() fits failed it these has specified
      parameter limits despite using an algorithm other than "port".
      (PR#15960)

    * Subclassing an S4 class failed if the class required arguments to
      the generator, through its initialize() method.

    * removeSource() did not properly handle expressions containing
      arguments that were supplied as missing, e.g.  x[i,]. (PR#15957)

    * as.environment(list()) now works, and as.list() of such an
      environment is now the same as list().

    * Several tcltk functions failed when run in unusual environments.
      (PR#15970)

    * options(list()) now works (trivially). (PR#15979)

    * merge(<dendrogram>, ..) now works correctly for two `independent'
      dendrograms (PR#15648), and still compatibly via adjust = "auto"
      e.g. for two branches of an existing dendrogram.

    * The plot method for "hclust" objects gets an optional argument
      check; When that is true (the default) it checks more carefully
      for valid input.

    * (Windows only) If a user chose to install 64 bit R but not 32 bit
      R, the bin/R and bin/Rscript executables failed to run.
      (PR#15981)

    * Various possible buffer overruns have been prevented, and missed
      memory protection added. (PR#15990)

    * Rscript no longer passes --args to R when there are no extra
      ("user") arguments.

    * objects like getClass("refClass")@prototype now print() and str()
      without error.

    * identical() now also looks at the S4 bit.

    * hist(x, breaks) is more robust in adding a small fuzz to few
      breaks when some are very large. (PR#15988)

    * sub() and gsub() did not handle regular expressions like "\s{2,}"
      properly if the text contained NA or non-ascii elements in a
      UTF-8 locale.  Part of this was due to a bug in the TRE library.
      (PR#16009)

    * RShowDoc("NEWS") now displays the PDF version.

    * Matrices and arrays with last dimension zero did not print at all
      or incompletely.  (PR#16012)

    * plot.histogram() and hence hist() now respect the xaxs, yaxs and
      lab graphics parameters.  (PR#16021)

    * bw.SJ(x) and other bw.*() no longer segfault when x contains
      non-finite values. (PR#16024)

    * R CMD Rd2pdf unintentionally ignored its --os option.

    * The internal method of download.file() was not reporting file
      sizes and progress correctly on files larger than 2GB (inherited
      from libxml2).  This is corrected for 64-bit builds (32-bit
      platforms may not support such files, but where possible will be
      supported in future versions of R).

    * Work around a bug in OS X Yosemite where key environment
      variables may be duplicated causing issues in subprocesses. The
      duplicates are now removed on R startup (via Rprofile).
      (PR#16042)

    * Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
      latest XQuartz.


To generate a diff of this commit:
cvs rdiff -u -r1.154 -r1.155 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.20 -r1.21 pkgsrc/math/R/PLIST
cvs rdiff -u -r1.63 -r1.64 pkgsrc/math/R/distinfo
cvs rdiff -u -r1.33 -r1.34 pkgsrc/math/R/patches/patch-ac
cvs rdiff -u -r1.17 -r1.18 pkgsrc/math/R/patches/patch-ad

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