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

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Branch: CURRENT, Version: 3.3.3nb1, Package name: R-3.3.3nb1, 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)


   2017-04-30 03:22:04 by Ryo ONODERA | Files touched by this commit (612) | Package updated
Log message:
Recursive revbump from boost update
   2017-04-21 15:14:05 by Jonathan Perkin | Files touched by this commit (1)
Log message:
Pull in required dependencies.
   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 IN R 3.3.3
NEW FEATURES

    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.

INSTALLATION on a UNIX-ALIKE

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

UTILITIES

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

DEPRECATED AND DEFUNCT

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

BUG FIXES

    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 \ 
maintainer.

    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:
CHANGES IN R 3.3.2:

  NEW FEATURES:

    * 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
      matrices.

    * 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.

  INSTALLATION and INCLUDED SOFTWARE:

    * 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.

  UTILITIES:

    * 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
      declarations.

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

  DEPRECATED AND DEFUNCT:

    * 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).

  BUG FIXES:

    * 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.
      (PR#17130)

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

    * axis(side, x = D) and hence Axis() and plot() now work correctly
      for "Date" and time objects D, even when "time goes \ 
backward",
      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.
      (PR#17155)

    * 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).
      (PR#17161)

    * 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.