./math/R, Statistical language for data analysis and graphics

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Branch: CURRENT, Version: 3.3.3, Package name: R-3.3.3, Maintainer: markd

R is a language which bears a passing resemblance to the S language
developed at AT&T Bell Laboratories. It provides support for a
variety of statistical and graphical analyses. R is a true
computer language which contains a number of control-flow
constructions for iteration and alternation. It allows users to
add additional functionality by defining new functions. On
platforms which support the dlopen (3) interface, Fortran and C
code can be linked and called at run time.

R is very close to S in both syntax and semantics, but is not identical.
Whether this is a bug or feature is an open question.

Required to run:
[converters/libiconv] [www/curl] [graphics/tiff] [graphics/png] [graphics/cairo] [graphics/jpeg] [lang/perl5] [lang/g95] [math/blas] [devel/gettext-lib] [devel/pcre] [devel/readline] [x11/tk]

Required to build:
[pkgtools/x11-links] [x11/glproto] [x11/renderproto] [x11/xproto] [x11/xf86vidmodeproto] [x11/xf86driproto] [x11/damageproto] [x11/inputproto] [x11/xextproto] [x11/dri2proto] [x11/xcb-proto] [x11/fixesproto4] [devel/libtool-fortran] [pkgtools/cwrappers]

Master sites: (Expand)

SHA1: 9e205a817970578ecd80384f397bae35b46f13b9
RMD160: 5f0d3aa3cf26132ac8774d2589083a12493c18ad
Filesize: 29105.787 KB

Version history: (Expand)

CVS history: (Expand)

   2017-03-11 10:50:35 by Wen Heping | Files touched by this commit (3) | Package updated
Log message:
Update to 3.3.3

Upstream changes:

    Changes when redirection of a http:// URL to a https:// URL is encountered:

        The internal methods of download.file() and url() now report that they \ 
cannot follow this (rather than failing silently).

        (Unix-alike) download.file(method = "auto") (the default) \ 
re-tries with method = "libcurl".

        (Unix-alike) url(method = "default") with an explicit open \ 
argument re-tries with method = "libcurl". This covers many of the \ 
usages, e.g. readLines() with a URL argument.


    The configure check for the zlib version is now robust to versions longer \ 
than 5 characters, including 1.2.11.


    Environmental variable _R_CHECK_TESTS_NLINES_ controls how R CMD check \ 
reports failing tests (see §8 of the ‘R Internals’ manual).


    (C-level Native routine registration.) The undocumented styles field of the \ 
components of R_CMethodDef and R_FortranMethodDef is deprecated.


    vapply(x, *) now works with long vectors x. (PR#17174)

    isS3method("is.na.data.frame") and similar are correct now. (PR#17171)

    grepRaw(<long>, <short>, fixed = TRUE) now works, thanks to a \ 
patch by Mikko Korpela. (PR#17132)

    Package installation into a library where the package exists via symbolic \ 
link now should work wherever Sys.readlink() works, resolving PR#16725.

    "Cincinnati" was missing an "n" in the precip dataset.

    Fix buffer overflow vulnerability in pdf() when loading an encoding file. \ 
Reported by Talos (TALOS-2016-0227).

    getDLLRegisteredRoutines() now produces its warning correctly when multiple \ 
DLLs match, thanks to Matt Dowle's PR#17184.

    Sys.timezone() now returns non-NA also on platforms such as Ubuntu 14.04.5 \ 
LTS, thanks to Mikko Korpela's PR#17186.

    format(x) for an illegal "POSIXlt" object x no longer segfaults.

    methods(f) now also works for f "(" or "{".

    (Windows only) dir.create() did not check the length of the path to create, \ 
and so could overflow a buffer and crash R. (PR#17206)

    On some systems, very small hexadecimal numbers in hex notation would \ 
underflow to zero. (PR#17199)

    pmin() and pmax() now work again for ordered factors and 0-length S3 classed \ 
objects, thanks to Suharto Anggono's PR#17195 and PR#17200.

    bug.report() did not do any validity checking on a package's BugReports \ 
field. It now ignores an empty field, removes leading whitespace and only \ 
attempts to open http:// and https:// URLs, falling back to emailing the \ 

    Bandwidth selectors bw.ucv() and bw.SJ() gave incorrect answers or \ 
incorrectly reported an error (because of integer overflow) for inputs longer \ 
than 46341. Similarly for bw.bcv() at length 5793.

    Another possible integer overflow is checked and may result in an error \ 
report (rather than an incorrect result) for much longer inputs (millions for a \ 
smooth distribution).

    findMethod() failed if the active signature had expanded beyond what a \ 
particular package used. (Example with packages XR and XRJulia on CRAN.)

    qbeta() underflowed too early in some very asymmetric cases. (PR#17178)

    R CMD Rd2pdf had problems with packages with non-ASCII titles in ‘.Rd’ \ 
files (usually the titles were omitted).
   2017-01-01 17:06:40 by Adam Ciarcinski | Files touched by this commit (616) | Package updated
Log message:
Revbump after boost update
   2016-11-06 03:08:17 by Wen Heping | Files touched by this commit (2) | Package updated
Log message:
Update to 3.3.2

Upstream changes:


    * extSoftVersion() now reports the version (if any) of the readline
      library in use.

    * The version of LAPACK included in the sources has been updated to
      3.6.1, a bug-fix release including a speedup for the
      non-symmetric case of eigen().

    * Use options(deparse.max.lines=) to limit the number of lines
      recorded in .Traceback and other deparsing activities.

    * format(<AsIs>) looks more regular, also for non-character atomic

    * abbreviate() gains an option named = TRUE.

    * The online documentation for package methods is extensively
      rewritten.  The goals are to simplify documentation for basic
      use, to note old features not recommended and to correct
      out-of-date information.

    * Calls to setMethod() no longer print a message when creating a
      generic function in those cases where that is natural: S3
      generics and primitives.


    * Versions of the readline library >= 6.3 had been changed so that
      terminal window resizes were not signalled to readline: code has
      been added using a explicit signal handler to work around that
      (when R is compiled against readline >= 6.3).  (PR#16604)

    * configure works better with Oracle Developer Studio 12.5.


    * R CMD check reports more dubious flags in files
      src/Makevars[.in], including -w and -g.

    * R CMD check has been set up to filter important warnings from
      recent versions of gfortran with -Wall -pedantic: this now
      reports non-portable GNU extensions such as out-of-order

    * R CMD config works better with paths containing spaces, even
      those of home directories (as reported by Ken Beath).


    * Use of the C/C++ macro NO_C_HEADERS is deprecated (no C headers
      are included by R headers from C++ as from R 3.3.0, so it should
      no longer be needed).


    * The check for non-portable flags in R CMD check could be stymied
      by src/Makevars files which contained targets.

    * (Windows only) When using certain desktop themes in Windows 7 or
      higher, Alt-Tab could cause Rterm to stop accepting input.
      (PR#14406; patch submitted by Jan Gleixner.)

    * pretty(d, ..) behaves better for date-time d (PR#16923).

    * When an S4 class name matches multiple classes in the S4 cache,
      perform a dynamic search in order to obey namespace imports.
      This should eliminate annoying messages about multiple hits in
      the class cache.  Also, pass along the package from the
      ClassExtends object when looking up superclasses in the cache.

    * sample(NA_real_) now works.

    * Packages using non-ASCII encodings in their code did not install
      data properly on systems using different encodings.

    * merge(df1, df2) now also works for data frames with column names
      "na.last", "decreasing", or "method".  (PR#17119)

    * contour() caused a segfault if the labels argument had length
      zero.  (Reported by Bill Dunlap.)

    * unique(warnings()) works more correctly, thanks to a new
      duplicated.warnings() method.

    * findInterval(x, vec = numeric(), all.inside = TRUE) now returns
      0s as documented.  (Reported by Bill Dunlap.)

    * (Windows only) R CMD SHLIB failed when a symbol in the resulting
      library had the same name as a keyword in the .def file.

    * pmax() and pmin() now work with (more ?)  classed objects, such
      as "Matrix" from the Matrix package, as documented for a long

    * axis(side, x = D) and hence Axis() and plot() now work correctly
      for "Date" and time objects D, even when "time goes \ 
      e.g., with decreasing xlim.  (Reported by William May.)

    * str(I(matrix(..))) now looks as always intended.

    * plot.ts(), the plot() method for time series, now respects cex,
      lwd and lty.  (Reported by Greg Werbin.)

    * parallel::mccollect() now returns a named list (as documented)
      when called with wait = FALSE.  (Reported by Michel Lang.)

    * If a package added a class to a class union in another package,
      loading the first package gave erroneous warnings about
      "undefined subclass".

    * c()'s argument use.names is documented now, as belonging to the
      (C internal) default method.  In "parallel", argument recursive
      is also moved from the generic to the default method, such that
      the formal argument list of base generic c() is just (...).

    * rbeta(4, NA) and similarly rgamma() and rnbinom() now return
      NaN's with a warning, as other r<dist>(), and as documented.

    * Using options(checkPackageLicense = TRUE) no longer requires
      acceptance of the licence for non-default standard packages such
      as compiler.  (Reported by Mikko Korpela.)

    * split(<very_long>, *) now works even when the split off parts are
      long. (PR#17139)

    * min() and max() now also work correctly when the argument list
      starts with character(0).  (PR#17160)

    * Subsetting very large matrices (prod(dim(.)) >= 2^31) now works
      thanks to Michael Schubmehl's PR#17158.

    * bartlett.test() used residual sums of squares instead of
      variances, when the argument was a list of lm objects.  (Reported
      by Jens Ledet Jensen).

    * plot(<lm>, which = *) now correctly labels the contour lines for
      the standardized residuals for which = 6.  It also takes the
      correct p in case of singularities (also for which = 5).

    * xtabs(~ exclude) no longer fails from wrong scope, thanks to
      Suharto Anggono's PR#17147.

    * Reference class calls to methods() did not re-analyse previously
      defined methods, meaning that calls to methods defined later
      would fail. (Reported by Charles Tilford).

    * findInterval(x, vec, left.open = TRUE) misbehaved in some cases.
      (Reported by Dmitriy Chernykh.)
   2016-10-07 20:26:14 by Adam Ciarcinski | Files touched by this commit (611) | Package updated
Log message:
Revbump post boost update
   2016-09-08 22:41:26 by Joerg Sonnenberger | Files touched by this commit (1)
Log message:
Override zlib 1.2.5 check in configure, it is not required. Unbreaks
NetBSD 7.0 and earlier.
   2016-08-15 11:36:32 by Jonathan Perkin | Files touched by this commit (1) | Package updated
Log message:
Update Darwin-specifix PLIST with new timezones.
   2016-07-26 06:53:33 by Wen Heping | Files touched by this commit (8) | Package updated
Log message:
Update to 3.3.1

Upstream changes:


    * R CMD INSTALL and hence install.packages() gave an internal error
      installing a package called description from a tarball on a
      case-insensitive file system.

    * match(x, t) (and hence x %in% t) failed when x was of length one,
      and either character and x and t only differed in their Encoding
      or when x and t where complex with NAs or NaNs.  (PR#16885.)

    * unloadNamespace(ns) also works again when ns is a 'namespace', as
      from getNamespace().

    * rgamma(1,Inf) or rgamma(1, 0,0) no longer give NaN but the
      correct limit.

    * length(baseenv()) is correct now.

    * pretty(d, ..) for date-time d rarely failed when "halfmonth" time
      steps were tried (PR#16923) and on 'inaccurate' platforms such as
      32-bit windows or a configuration with --disable-long-double; see
      comment #15 of PR#16761.

    * In text.default(x, y, labels), the rarely(?) used default for
      labels is now correct also for the case of a 2-column matrix x
      and missing y.

    * as.factor(c(a = 1L)) preserves names() again as in R < 3.1.0.

    * strtrim(""[0], 0[0]) now works.

    * Use of Ctrl-C to terminate a reverse incremental search started
      by Ctrl-R in the readline-based Unix terminal interface is now
      supported for readline >= 6.3 (Ctrl-G always worked).  (PR#16603)

    * diff(<difftime>) now keeps the "units" attribute, as \ 
      already did, PR#16940.



    * nchar(x, *)'s argument keepNA governing how the result for NAs in
      x is determined, gets a new default keepNA = NA which returns NA
      where x is NA, except for type = "width" which still returns 2,
      the formatting / printing width of NA.

    * All builds have support for https: URLs in the default methods
      for download.file(), url() and code making use of them.

      Unfortunately that cannot guarantee that any particular https:
      URL can be accessed.  For example, server and client have to
      successfully negotiate a cryptographic protocol (TLS/SSL, ...)
      and the server's identity has to be verifiable _via_ the
      available certificates.  Different access methods may allow
      different protocols or use private certificate bundles: we
      encountered a https: CRAN mirror which could be accessed by one
      browser but not by another nor by download.file() on the same
      Linux machine.


    * The print method for methods() gains a byclass argument.

    * New functions validEnc() and validUTF8() to give access to the
      validity checks for inputs used by grep() and friends.

    * Experimental new functionality for S3 method checking, notably

      Also, the names of the R 'language elements' are exported as
      character vector tools::langElts.

    * str(x) now displays "Time-Series" also for matrix (multivariate)
      time-series, i.e. when is.ts(x) is true.

    * (Windows only) The GUI menu item to install local packages now
      accepts *.tar.gz files as well as *.zip files (but defaults to
      the latter).

    * New programmeR's utility function chkDots().

    * D() now signals an error when given invalid input, rather than
      silently returning NA.  (Request of John Nash.)

    * formula objects are slightly more "first class": e.g., formula()
      or new("formula", y ~ x) are now valid.  Similarly, for \ 
      "ordered" and "summary.table".  Packages defining S4 \ 
classes with
      the above S3/S4 classes as slots should be reinstalled.

    * New function strrep() for repeating the elements of a character

    * rapply() preserves attributes on the list when how = "replace".

    * New S3 generic function sigma() with methods for extracting the
      estimated standard deviation aka "residual standard deviation"
      from a fitted model.

    * news() now displays R and package news files within the HTML help
      system if it is available.  If no news file is found, a visible
      NULL is returned to the console.

    * as.raster(x) now also accepts raw arrays x assuming values in

    * Subscripting of matrix/array objects of type "expression" is now

    * type.convert("i") now returns a factor instead of a complex value
      with zero real part and missing imaginary part.

    * Graphics devices cairo_pdf() and cairo_ps() now allow non-default
      values of the cairographics 'fallback resolution' to be set.

      This now defaults to 300 on all platforms: that is the default
      documented by cairographics, but apparently was not used by all
      system installations.

    * file() gains an explicit method argument rather than implicitly
      using getOption("url.method", "default").

    * Thanks to a patch from Tomas Kalibera, x[x != 0] is now typically
      faster than x[which(x != 0)] (in the case where x has no NAs, the
      two are equivalent).

    * read.table() now always uses the names for a named colClasses
      argument (previously names were only used when colClasses was too
      short). (In part, wish of PR#16478.)

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

    * The out-of-the box Bioconductor mirror has been changed to one
      using https://: use chooseBioCmirror() to choose a http:// mirror
      if required.

    * The data frame and formula methods for aggregate() gain a drop

    * available.packages() gains a repos argument.

    * The undocumented switching of methods for url() on https: and
      ftps: URLs is confined to method = "default" (and documented).

    * smoothScatter() gains a ret.selection argument.

    * qr() no longer has a ... argument to pass additional arguments to

    * [ has a method for class "table".

    * It is now possible (again) to replayPlot() a display list
      snapshot that was created by recordPlot() in a different R

      It is still not a good idea to use snapshots as a persistent
      storage format for R plots, but it is now not completely silly to
      use a snapshot as a format for transferring an R plot between two
      R sessions.

      The underlying changes mean that packages providing graphics
      devices (e.g., Cairo, RSvgDevice, cairoDevice, tikzDevice) will
      need to be reinstalled.

      Code for restoring snapshots was contributed by Jeroen Ooms and
      JJ Allaire.

      Some testing code is available at <URL:

    * tools::undoc(dir = D) and codoc(dir = D) now also work when D is
      a directory whose normalizePath()ed version does not end in the
      package name, e.g. from a symlink.

    * abbreviate() has more support for multi-byte character sets - it
      no longer removes bytes within characters and knows about Latin
      vowels with accents.  It is still only really suitable for (most)
      European languages, and still warns on non-ASCII input.

      abbreviate(use.classes = FALSE) is now implemented, and that is
      more suitable for non-European languages.

    * match(x, table) is faster (sometimes by an order of magnitude)
      when x is of length one and incomparables is unchanged, thanks to
      Peter Haverty (PR#16491).

    * More consistent, partly not back-compatible behavior of NA and
      NaN coercion to complex numbers, operations less often resulting
      in complex NA (NA_complex_).

    * lengths() considers methods for length and [[ on x, so it should
      work automatically on any objects for which appropriate methods
      on those generics are defined.

    * The logic for selecting the default screen device on OS X has
      been simplified: it is now quartz() if that is available even if
      environment variable DISPLAY has been set by the user.

      The choice can easily be overridden _via_ environment variable

    * On Unix-like platforms which support the getline C library
      function, system(*,intern = TRUE) no longer truncates (output)
      lines longer than 8192 characters, thanks to Karl Millar.

    * rank() gains a ties.method = "last" option, for convenience (and

    * regmatches(invert = NA) can now be used to extract both
      non-matched and matched substrings.

    * data.frame() gains argument fix.empty.names; as.data.frame.list()
      gets new cut.names, col.names and fix.empty.names.

    * plot(x ~ x, *) now warns that it is the same as plot(x ~ 1, *).

    * recordPlot() has new arguments load and attach to allow package
      names to be stored as part of a recorded plot.  replayPlot() has
      new argument reloadPkgs to load/attach any package names that
      were stored as part of a recorded plot.

    * S4 dispatch works within calls to .Internal(). This means
      explicit S4 generics are no longer needed for unlist() and

    * Only font family names starting with "Hershey" (and not \ 
"Her" as
      before) are given special treatment by the graphics engine.

    * S4 values are automatically coerced to vector (via as.vector)
      when subassigned into atomic vectors.

    * findInterval() gets a left.open option.

    * The version of LAPACK included in the sources has been updated to
      3.6.0, including those 'deprecated' routines which were
      previously included.  _Ca_ 40 double-complex routines have been
      added at the request of a package maintainer.

      As before, the details of what is included are in
      src/modules/lapack/README and this now gives information on
      earlier additions.

    * tapply() has been made considerably more efficient without
      changing functionality, thanks to proposals from Peter Haverty
      and Suharto Anggono.  (PR#16640)

    * match.arg(arg) (the one-argument case) is faster; so is
      sort.int().  (PR#16640)

    * The format method for object_size objects now also accepts
      "binary" units such as "KiB" and e.g., "Tb". \ 
 (Partly from

    * Profiling now records calls of the form foo::bar and some similar
      cases directly rather than as calls to <Anonymous>.  Contributed
      by Winston Chang.

    * New string utilities startsWith(x, prefix) and endsWith(x,
      suffix).  Also provide speedups for some grepl("^...",*) uses
      (related to proposals in PR#16490).

    * Reference class finalizers run at exit, as well as on garbage

    * Avoid parallel dependency on stats for port choice and random
      number seeds.  (PR#16668)

    * The radix sort algorithm and implementation from data.table
      (forder) replaces the previous radix (counting) sort and adds a
      new method for order().  Contributed by Matt Dowle and Arun
      Srinivasan, the new algorithm supports logical, integer (even
      with large values), real, and character vectors.  It outperforms
      all other methods, but there are some caveats (see ?sort).

    * The order() function gains a method argument for choosing between
      "shell" and "radix".

    * New function grouping() returns a permutation that stably
      rearranges data so that identical values are adjacent.  The
      return value includes extra partitioning information on the
      groups.  The implementation came included with the new radix

    * rhyper(nn, m, n, k) no longer returns NA when one of the three
      parameters exceeds the maximal integer.

    * switch() now warns when no alternatives are provided.

    * parallel::detectCores() now has default logical = TRUE on all
      platforms - as this was the default on Windows, this change only
      affects Sparc Solaris.

      Option logical = FALSE is now supported on Linux and recent
      versions of OS X (for the latter, thanks to a suggestion of Kyaw

    * hist() for "Date" or "POSIXt" objects would sometimes give
      misleading labels on the breaks, as they were set to the day
      before the start of the period being displayed.  The display
      format has been changed, and the shift of the start day has been
      made conditional on right = TRUE (the default).  (PR#16679)

    * R now uses a new version of the logo (donated to the R Foundation
      by RStudio).  It is defined in .svg format, so will resize
      without unnecessary degradation when displayed on HTML
      pages-there is also a vector PDF version.  Thanks to Dirk
      Eddelbuettel for producing the corresponding X11 icon.

    * New function .traceback() returns the stack trace which
      traceback() prints.

    * lengths() dispatches internally.

    * dotchart() gains a pt.cex argument to control the size of points
      separately from the size of plot labels.  Thanks to Michael
      Friendly and Milan Bouchet-Valat for ideas and patches.

    * as.roman(ch) now correctly deals with more diverse character
      vectors ch; also arithmetic with the resulting roman numbers
      works in more cases.  (PR#16779)

    * prcomp() gains a new option rank. allowing to directly aim for
      less than min(n,p) PC's.  The summary() and its print() method
      have been amended, notably for this case.

    * gzcon() gains a new option text, which marks the connection as
      text-oriented (so e.g. pushBack() works).  It is still always
      opened in binary mode.

    * The import() namespace directive now accepts an argument except
      which names symbols to exclude from the imports. The except
      expression should evaluate to a character vector (after
      substituting symbols for strings). See Writing R Extensions.

    * New convenience function Rcmd() in package tools for invoking R
      CMD tools from within R.

    * New functions makevars_user() and makevars_site() in package
      tools to determine the location of the user and site specific
      Makevars files for customizing package compilation.


    * R CMD check has a new option --ignore-vignettes for use with
      non-Sweave vignettes whose VignetteBuilder package is not

    * R CMD check now by default checks code usage (_via_ codetools)
      with only the base package attached.  Functions from default
      packages other than base which are used in the package code but
      not imported are reported as undefined globals, with a suggested
      addition to the NAMESPACE file.

    * R CMD check --as-cran now also checks DOIs in package CITATION
      and Rd files.

    * R CMD Rdconv and R CMD Rd2pdf each have a new option
      --RdMacros=pkglist which allows Rd macros to be specified before


    * The previously included versions of zlib, bzip2, xz and PCRE have
      been removed, so suitable external (usually system) versions are
      required (see the 'R Installation and Administration' manual).

    * The unexported and undocumented Windows-only devices cairo_bmp(),
      cairo_png() and cairo_tiff() have been removed.  (These devices
      should be used as e.g. bmp(type = "cairo").)

    * (Windows only) Function setInternet2() has no effect and will be
      removed in due course.  The choice between methods "internal" and
      "wininet" is now made by the method arguments of url() and
      download.file() and their defaults can be set _via_ options.  The
      out-of-the-box default remains "wininet" (as it has been since R

    * [<- with an S4 value into a list currently embeds the S4 object
      into its own list such that the end result is roughly equivalent
      to using [[<-.  That behavior is deprecated.  In the future, the
      S4 value will be coerced to a list with as.list().

    * Package tools' functions package.dependencies(), pkgDepends(),
      etc are deprecated now, mostly in favor of package_dependencies()
      which is both more flexible and efficient.


    * Support for very old versions of valgrind (e.g., 3.3.0) has been

    * The included libtool script (generated by configure) has been
      updated to version 2.4.6 (from 2.2.6a).

    * libcurl version 7.28.0 or later with support for the https
      protocol is required for installation (except on Windows).

    * BSD networking is now required (except on Windows) and so
      capabilities("http/ftp") is always true.

    * configure uses pkg-config for PNG, TIFF and JPEG where this is
      available.  This should work better with multiple installs and
      with those using static libraries.

    * The minimum supported version of OS X is 10.6 ('Snow Leopard'):
      even that has been unsupported by Apple since 2012.

    * The configure default on OS X is --disable-R-framework: enable
      this if you intend to install under /Library/Frameworks and use
      with R.app.

    * The minimum preferred version of PCRE has since R 3.0.0 been 8.32
      (released in Nov 2012).  Versions 8.10 to 8.31 are now deprecated
      (with warnings from configure), but will still be accepted until
      R 3.4.0.

    * configure looks for C functions __cospi, __sinpi and __tanpi and
      uses these if cospi _etc_ are not found.  (OS X is the main

    * (Windows) R is now built using gcc 4.9.3.  This build will
      require recompilation of at least those packages that include C++
      code, and possibly others.  A build of R-devel using the older
      toolchain will be temporarily available for comparison purposes.

      During the transition, the environment variable R_COMPILED_BY has
      been defined to indicate which toolchain was used to compile R
      (and hence, which should be used to compile code in packages).
      The COMPILED_BY variable described below will be a permanent
      replacement for this.

    * (Windows) A make and R CMD config variable named COMPILED_BY has
      been added.  This indicates which toolchain was used to compile R
      (and hence, which should be used to compile code in packages).


    * The make macro AWK which used to be made available to files such
      as src/Makefile is no longer set.


    * The API call logspace_sum introduced in R 3.2.0 is now remapped
      as an entry point to Rf_logspace_sum, and its first argument has
      gained a const qualifier.  (PR#16470)

      Code using it will need to be reinstalled.

      Similarly, entry point log1pexp also defined in Rmath.h is
      remapped there to Rf_log1pexp

    * R_GE_version has been increased to 11.

    * New API call R_orderVector1, a faster one-argument version of

    * When R headers such as R.h and Rmath.h are called from C++ code
      in packages they include the C++ versions of system headers such
      as <cmath> rather than the legacy headers such as <math.h>.
      (Headers Rinternals.h and Rinterface.h already did, and inclusion
      of system headers can still be circumvented by defining
      NO_C_HEADERS, including as from this version for those two

      The manual has long said that R headers should *not* be included
      within an extern "C" block, and almost all the packages affected
      by this change were doing so.

    * Including header S.h from C++ code would fail on some platforms,
      and so gives a compilation error on all.

    * The deprecated header Rdefines.h is now compatible with defining

    * The connections API now includes a function R_GetConnection()
      which allows packages implementing connections to convert R
      connection objects to Rconnection handles used in the API. Code
      which previously used the low-level R-internal getConnection()
      entry point should switch to the official API.


    * C-level asChar(x) is fixed for when x is not a vector, and it
      returns "TRUE"/"FALSE" instead of \ 
"T"/"F" for logical vectors.

    * The first arguments of .colSums() etc (with an initial dot) are
      now named x rather than X (matching colSums()): thus error
      messages are corrected.

    * A coef() method for class "maov" has been added to allow vcov()
      to work with multivariate results. (PR#16380)

    * method = "libcurl" connections signal errors rather than
      retrieving HTTP error pages (where the ISP reports the error).

    * xpdrows.data.frame() was not checking for unique row names; in
      particular, this affected assignment to non-existing rows via
      numerical indexing. (PR#16570)

    * tail.matrix() did not work for zero rows matrices, and could
      produce row "labels" such as "[1e+05,]".

    * Data frames with a column named "stringsAsFactors" now format and
      print correctly.  (PR#16580)

    * cor() is now guaranteed to return a value with absolute value
      less than or equal to 1. (PR#16638)

    * Array subsetting now keeps names(dim(.)).

    * Blocking socket connection selection recovers more gracefully on
      signal interrupts.

    * The data.frame method of rbind() construction row.names works
      better in borderline integer cases, but may change the names
      assigned.  (PR#16666)

    * (X11 only) getGraphicsEvent() miscoded buttons and missed mouse
      motion events.  (PR#16700)

    * methods(round) now also lists round.POSIXt.

    * tar() now works with the default files = NULL.  (PR#16716)

    * Jumps to outer contexts, for example in error recovery, now make
      intermediate jumps to contexts where on.exit() actions are
      established instead of trying to run all on.exit() actions before
      jumping to the final target. This unwinds the stack gradually,
      releases resources held on the stack, and significantly reduces
      the chance of a segfault when running out of C stack space. Error
      handlers established using withCallingHandlers() and
      options("error") specifications are ignored when handling a C
      stack overflow error as attempting one of these would trigger a
      cascade of C stack overflow errors.  (These changes resolve

    * The spacing could be wrong when printing a complex array.
      (Report and patch by Lukas Stadler.)

    * pretty(d, n, min.n, *) for date-time objects d works again in
      border cases with large min.n, returns a labels attribute also
      for small-range dates and in such cases its returned length is
      closer to the desired n.  (PR#16761) Additionally, it finally
      does cover the range of d, as it always claimed.

    * tsp(x) <- NULL did not handle correctly objects inheriting from
      both "ts" and "mts".  (PR#16769)

    * install.packages() could give false errors when
      options("pkgType") was "binary".  (Reported by Jose Claudio

    * A bug fix in R 3.0.2 fixed problems with locator() in X11, but
      introduced problems in Windows.  Now both should be fixed.

    * download.file() with method = "wininet" incorrectly warned of
      download file length difference when reported length was unknown.

    * diag(NULL, 1) crashed because of missed type checking.
   2016-07-09 08:39:18 by Thomas Klausner | Files touched by this commit (1068) | Package updated
Log message:
Bump PKGREVISION for perl-5.24.0 for everything mentioning perl.