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

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Branch: CURRENT, Version: 4.0.3nb1, Package name: R-4.0.3nb1, Maintainer: pkgsrc-users

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] [math/lapack] [math/blas] [devel/glib2] [devel/pango] [devel/gettext-lib] [devel/pcre] [devel/readline] [x11/tk] [lang/gcc7]

Required to build:
[pkgtools/x11-links] [x11/xcb-proto] [devel/libtool-fortran] [pkgtools/cwrappers] [x11/xorgproto]

Master sites: (Expand)

SHA1: 5daba2d63e07a9f39d9b69b68f0642d71213ec5c
RMD160: dd6fac10033746e5e0dd4fb0200b9008695e58e5
Filesize: 32711.924 KB

Version history: (Expand)

CVS history: (Expand)

   2021-01-09 03:14:06 by Makoto Fujiwara | Files touched by this commit (1)
Log message:
(math/R) Ignore the warnings from autoreconf
   2020-10-12 23:52:05 by Jason Bacon | Files touched by this commit (87) | Package updated
Log message:
math/blas, math/lapack: Install interchangeable BLAS system

Install the new interchangeable BLAS system created by Thomas Orgis,
currently supporting Netlib BLAS/LAPACK, OpenBLAS, cblas, lapacke, and
Apple's Accelerate.framework.  This system allows the user to select any
BLAS implementation without modifying packages or using package options, by
setting PKGSRC_BLAS_TYPES in mk.conf. See mk/blas.buildlink3.mk for details.

This commit should not alter behavior of existing packages as the system
defaults to Netlib BLAS/LAPACK, which until now has been the only supported


Add new mk/blas.buildlink3.mk for inclusion in dependent packages
Install compatible Netlib math/blas and math/lapack packages
Update math/blas and math/lapack MAINTAINER approved by adam@
OpenBLAS, cblas, and lapacke will follow in separate commits
Update direct dependents to use mk/blas.buildlink3.mk
Perform recursive revbump
   2020-10-11 17:22:56 by Wen Heping | Files touched by this commit (2) | Package updated
Log message:
Update to 4.0.3



    * On platforms using configure option --with-internal-tzcode,
      additional values "internal" and (on macOS only) \ 
"macOS" are
      accepted for the environment variable TZDIR.  (See ?TZDIR.)

      On macOS, "macOS" is used by default if the system timezone
      database is a newer version than that in the R installation.

    * When install.packages(type = "source") fails to find a package in
      a repository it mentions package versions which are excluded by
      their R version requirement and links to hints on why a package
      might not be found.

    * The default value for options("timeout") can be set from
      enviromnent variable R_DEFAULT_INTERNET_TIMEOUT, still defaulting
      to 60 (seconds) if that is not set or invalid.

      This may be needed when child R processes are doing downloads,
      for example during the installation of source packages which
      download jars or other forms of data.


    * There is now support for parallelized Link-Time Optimization
      (LTO) with GCC and for 'thin' LTO with clang _via_ setting the
      LTO macro.

    * There is support for setting a different LTO flag for the Fortran
      compiler, including to empty when mixing clang and gfortran (as
      on macOS).  See file config.site.

    * There is a new LTO_LD macro to set linker options for LTO
      compilation, for example to select an alternative linker or to
      parallelize thin LTO.


    * The LINPACK argument to chol.default(), chol2inv(),
      solve.default() and svd() has been defunct since R 3.1.0.  Using
      it now gives a warning which will become an error in R 4.1.0.


    * The code mitigating stack overflow with PCRE regexps on very long
      strings is enabled for PCRE2 < 10.30 also when JIT is enabled,
      since stack overflows have been seen in that case.

    * Fix to correctly show the group labels in dotchart() (which where
      lost in the ylab improvement for R 4.0.0).

    * addmargins(*, ..) now also works when fn() is a local function,
      thanks to bug report and patch PR#17124 from Alex Bertram.

    * rank(x) and hence sort(x) now work when x is an object (as per
      is.object(x)) of type "raw" _and_ provides a valid `[` method,
      e.g., for gmp::as.bigz(.) numbers.

    * chisq.test(*, simulate.p.value=TRUE) and r2dtable() now work
      correctly for large table entries (in the millions).  Reported by
      Sebastian Meyer and investigated by more helpers in PR#16184.

    * Low-level socket read/write operations have been fixed to
      correctly signal communication errors. Previously, such errors
      could lead to a segfault due to invalid memory access. Reported
      and debugged by Dmitriy Selivanov in PR#17850.

    * quantile(x, pr) works more consistently for pr values slightly
      outside [0,1], thanks to Suharto Anggono's PR#17891.

      Further, quantile(x, prN, names=FALSE) now works even when prN
      contains NAs, thanks to Anggono's PR#17892.  Ditto for ordered
      factors or Date objects when type = 1 or 3, thanks to PR#17899.

    * Libcurl-based internet access, including curlGetHeaders(), was
      not respecting the "timeout" option.  If this causes
      unanticipated timeouts, consider increasing the default by

    * as.Date(<char>) now also works with an initial "", thanks to
      Michael Chirico's PR#17909.

    * isS3stdGeneric(f) now detects an S3 generic also when it it is
      trace()d, thanks to Gabe Becker's PR#17917.

    * R_allocLD() has been fixed to return memory aligned for long
      double type PR#16534.

    * fisher.test() no longer segfaults when called again after its
      internal stack has been exceeded PR#17904.

    * Accessing a long vector represented by a compact integer sequence
      no longer segfaults (reported and debugged by Hugh Parsonage).

    * duplicated() now works also for strings with multiple encodings
      inside a single vector PR#17809.

    * phyper(11, 15, 0, 12, log.p=TRUE) no longer gives NaN; reported
      as PR#17271 by Alexey Stukalov.

    * Fix incorrect calculation in logLik.nls() PR#16100, patch from
      Sebastian Meyer.

    * A very old bug could cause a segfault in model.matrix() when
      terms involved logical variables.  Part of PR#17879.

    * model.frame.default() allowed data = 1, leading to involuntary
      variable capture (rest of PR#17879).

    * tar() no longer skips non-directory files, thanks to a patch by
      Sebastian Meyer, fixing the remaining part of PR#16716.
   2020-08-31 20:13:29 by Thomas Klausner | Files touched by this commit (3631) | Package updated
Log message:
*: bump PKGREVISION for perl-5.32.
   2020-08-17 22:20:41 by Leonardo Taccari | Files touched by this commit (2202)
Log message:
*: revbump after fontconfig bl3 changes (libuuid removal)
   2020-07-31 19:04:12 by Brook Milligan | Files touched by this commit (1)
Log message:
Conditionally define WRKSRC.

Conditionally define WRKSRC so that R packages with an unusual organization
can override the default.
   2020-07-17 13:46:09 by Jonathan Perkin | Files touched by this commit (1) | Package updated
Log message:
R: Fix PLIST.Darwin for previous update.
   2020-07-16 04:22:55 by Mark Davies | Files touched by this commit (3) | Package updated
Log message:
R: update to 4.0.2



    * Packages need to be (re-)installed under this version (4.0.0) of

    * matrix objects now also inherit from class "array", so e.g.,
      class(diag(1)) is c("matrix", "array").  This \ 
invalidates code
      incorrectly assuming that class(matrix_obj)) has length one.

      S3 methods for class "array" are now dispatched for matrix

    * There is a new syntax for specifying _raw_ character constants
      similar to the one used in C++: r"(...)" with ... any character
      sequence not containing the sequence )".  This makes it easier to
      write strings that contain backslashes or both single and double
      quotes.  For more details see ?Quotes.

    * R now uses a stringsAsFactors = FALSE default, and hence by
      default no longer converts strings to factors in calls to
      data.frame() and read.table().

      A large number of packages relied on the previous behaviour and
      so have needed/will need updating.

    * The plot() S3 generic function is now in package base rather than
      package graphics, as it is reasonable to have methods that do not
      use the graphics package.  The generic is currently re-exported
      from the graphics namespace to allow packages importing it from
      there to continue working, but this may change in future.

      Packages which define S4 generics for plot() should be
      re-installed and package code using such generics from other
      packages needs to ensure that they are imported rather than rely
      on their being looked for on the search path (as in a namespace,
      the base namespace has precedence over the search path).

See ${PREFIX}/lib/R/doc/NEWS for full changes.