Log message:
math/R: fix compiler flags embedded within Makeconf

The R package installs the file lib/R/etc/Makeconf, which is intended
to be used by R packages that themselves compile programs.  This
feature is rarely used, but the math/R-nimble package is an example of
one that does.  For this to work, the compiler flags embedded within
Makeconf must be compatible with the system compiler.  At least on
MacOS, this is not the case by default, and so nimble compilations
fail.  This substitutes ${COMPILER_RPATH_FLAG} into configure.ac, so
that it is used when creating Makeconf.  Since neither R itself nor
most R packages compile other programs, Makeconf is generally not used
and this fix will have no impact.

Log message:
Update to 4.1.3

Upstream changes:
CHANGES IN R 4.1.3:

  NEW FEATURES:

    * The default version of Bioconductor has been changed to 3.14.
      (This is used by setRepositories and the menus in GUIs.)

  UTILITIES:

    * R CMD check --as-cran has a workaround for a bug in versions of
      file up to at least 5.41 which mis-identify DBF files last
      changed in 2022 as executables.

  C-LEVEL FACILITIES:

    * The legacy S-compatibility macros SINGLE_* in R_ext/Constants.h
      (included by R.h) are deprecated and will be removed in R 4.2.0.

  BUG FIXES:

    * Initialization of self-starting nls() models with initialization
      functions following the pre-R-4.1.0 API (without the ...
      argument) works again for now, with a deprecation warning.

    * Fixed quoting of ~autodetect~ in Java setting defaults to avoid
      inadvertent user lookup due to leading ~, reported in PR#18231 by
      Harold Gutch.

    * substr(., start, stop) <- v now treats _negative_ stop values
      correctly.  Reported with a patch in PR#18228 by Brodie Gaslam.

    * Subscripting an array x without dimnames by a
      length(dim(x))-column character matrix gave "random" non-sense,
      now an error; reported in PR#18244 by Mikael Jagan.

    * ...names() now matches names(list(...)) closely, fixing PR#18247.

    * all.equal(*, scale = s) now works as intended when length(s) > 1,
      partly thanks to Michael Chirico's PR#18272.

    * print(x) for long vectors x now also works for named atomic
      vectors or lists and prints the correct number when reaching the
      getOption("max.print") limit; partly thanks to a report and
      proposal by Hugh Parsonage to the R-devel list.

    * all.equal(<selfStart>, *) no longer signals a deprecation
      warning.

    * reformulate(*, response=r) gives a helpful error message now when
      length(r) > 1, thanks to Bill Dunlap's PR#18281.

    * Modifying globalCallingHandlers inside withCallingHandlers() now
      works or fails correctly, thanks to Henrik Bengtsson's PR#18257.

    * hist(<Date>, breaks = "days") and hist(<POSIXt>, \ 
breaks = "secs")
      no longer fail for inputs of length 1.

    * qbeta(.001, .9, .009) and similar cases now converge correctly
      thanks to Ben Bolker's report in PR#17746.

    * window(x, start, end) no longer wrongly signals "'start' cannot
      be after 'end'", fixing PR#17527 and PR#18291.

    * data() now checks that its (rarely used) list argument is a
      character vector - a couple of packages passed other types and
      gave incorrect results.

    * which() now checks its arr.ind argument is TRUE rather coercing
      to logical and taking the first element - which gave incorrect
      results in package code.

    * model.weights() and model.offset() more carefully extract their
      model components, thanks to Ben Bolker and Tim Taylor's R-devel
      post.

    * list.files(recursive = TRUE) now shows all broken symlinks
      (previously, some of them may have been omitted, PR#18296).

Log message:
revbump for icu and libffi

Log message:
R: Fix PLIST.Darwin yet again.

Add a comment to the Makefile to hopefully avoid macOS users constantly being
broken on every update.

Log message:
Update to 4.1.2

Upstream changes:
CHANGES IN R 4.1.2:

  C-LEVEL FACILITIES:

    * The workaround in headers R.h and Rmath.h (using namespace std;)
      for the Oracle Developer Studio compiler is no longer needed now
      C++11 is required so has been removed.  A couple more usages of
      log() (which should have been std::log()) with an int argument
      are reported on Solaris.

    * The undocumented limit of 4095 bytes on messages from the
      S-compatibility macros PROBLEM and MESSAGE is now documented and
      longer messages will be silently truncated rather than
      potentially causing segfaults.

    * If the R_NO_SEGV_HANDLER environment variable is non-empty, the
      signal handler for SEGV/ILL/BUS signals (which offers recovery
      user interface) is not set. This allows more reliable debugging
      of crashes that involve the console.

  DEPRECATED AND DEFUNCT:

    * The legacy S-compatibility macros PROBLEM, MESSAGE, ERROR, WARN,
      WARNING, RECOVER, ... are deprecated and will be hidden in R
      4.2.0. R's native interface of Rf_error and Rf_warning has long
      been preferred.

  BUG FIXES:

    * .mapply(F, dots, .) no longer segfaults when dots is not a list
      and uses match.fun(F) as always documented; reported by Andrew
      Simmons in PR#18164.

    * hist(<Date>, ...) and hist(<POSIXt>, ...)  no longer pass
      arguments for rect() (such as col and density) to axis().
      (Thanks to Sebastian Meyer's PR#18171.)

    * \Sexpr{ch} now preserves Encoding(ch). (Thanks to report and
      patch by Jeroen Ooms in PR#18152.)

    * Setting the RNG to "Marsaglia-Multicarry" e.g., by RNGkind(), now
      warns in more places, thanks to Andr'e Gillibert's report and
      patch in PR#18168.

    * gray(numeric(), alpha=1/2) no longer segfaults, fixing PR#18183,
      reported by Till Krenz.

    * Fixed dnbinom(x, size=<very_small>, .., log=TRUE) regression,
      reported by Martin Morgan.

    * as.Date.POSIXlt(x) now keeps names(x), thanks to Davis Vaughan's
      report and patch in PR#18188.

    * model.response() now strips an "AsIs" class typically, thanks to
      Duncan Murdoch's report and other discussants in PR#18190.

    * try() is considerably faster in case of an error and long call,
      as e.g., from some do.call().  Thanks to Alexander Kaever's
      suggestion posted to R-devel.

    * qqline(y = <object>) such as y=I(.), now works, see also
      PR#18190.

    * Non-integer mgp par() settings are now handled correctly in
      axis() and mtext(), thanks to Mikael Jagan and Duncan Murdoch's
      report and suggestion in PR#18194.

    * formatC(x) returns length zero character() now, rather than ""
      when x is of length zero, as documented, thanks to Davis
      Vaughan's post to R-devel.

    * removeSource(fn) now retains (other) attributes(fn).

Log message:
math: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes

Log message:
math: Remove SHA1 hashes for distfiles

Log message:
revbump for boost-libs

Log message:
Update to 4.1.1

Upstream changes:
CHANGES IN R 4.1.1:

  NEW FEATURES:

    * require(pkg, quietly = TRUE) is quieter and in particular does
      not warn if the package is not found.

  DEPRECATED AND DEFUNCT:

    * Use of ftp:// URIs should be regarded as deprecated, with
      on-going support confined to method = "libcurl" and not routinely
      tested.  (Nowadays no major browser supports them.)

    * The non-default method = "internal" is deprecated for http:// and
      ftp:// URIs for both download.file and url.

    * On Windows, method = "wininet" is deprecated for http://,
      https:// and ftp:// URIs for both download.file and url.  (A
      warning is only given for ftp://.)

      For ftp:// URIs the default method is now "libcurl" if available
      (which it is on CRAN builds).

      method = "wininet" remains the default for http:// and https://
      URIs but if libcurl is available, using method = "libcurl" is
      preferred.

  INSTALLATION:

    * make check now works also without a LaTeX installation.  (Thanks
      to Sebastian Meyer's PR#18103.)

  BUG FIXES:

    * make check-devel works again in an R build configured with
      --without-recommended-packages.

    * qnbinom(p, size, mu) for large size/mu is correct now in a range
      of cases (PR#18095); similarly for the (size, prob)
      parametrization of the negative binomial.  Also qpois() and
      qbinom() are better and or faster for extreme cases.  The
      underlying C code has been modularized and is common to all four
      cases of discrete distributions.

    * gap.axis is now part of the axis() arguments which are passed
      from bxp(), and hence boxplot().  (Thanks to Martin Smith's
      report and suggestions in PR#18109.)

    * .First and .Last can again be set from the site profile.

    * seq.int(from, to, *) and seq.default(..) now work better in large
      range cases where from-to is infinite where the two boundaries
      are finite.

    * all.equal(x,y) now returns TRUE correctly also when several
      entries of abs(x) and abs(y) are close to .Machine$double.xmax,
      the largest finite numeric.

    * model.frame() now clears the object bit when removing the class
      attribute of a value via na.action (PR#18100).

    * charClass() now works with multi-character strings on Windows
      (PR#18104, fixed by Bill Dunlap).

    * encodeString() on Solaris now works again in Latin-1 encoding on
      characters represented differently in UTF-8.  Support for
      surrogate pairs on Solaris has been improved.

    * file.show() on Windows now works with non-ASCII path names
      representable in the current native encoding (PR#18132).

    * Embedded R on Windows can now find R home directory via the
      registry even when installed only for the current user
      (PR#18135).

    * pretty(x) with finite x now returns finite values also in the
      case where the extreme x values are close in size to the maximal
      representable number .Machine$double.xmax.

      Also, it's been tweaked for very small ranges and when a boundary
      is close (or equal) to zero; e.g., pretty(c(0,1e-317)) no longer
      has negative numbers, currently still warning about a very small
      range, and pretty(2^-(1024 - 2^-1/(c(24,10)))) is more accurate.

    * The error message for not finding vignette files when weaving has
      correct file sizes now. (Thanks to Sebastian Meyer's PR#18154.)

    * dnbinom(20, <large>, 1) now correctly gives 0, and similar cases
      are more accurate with underflow precaution.  (Reported by
      Francisco Vera Alcivar in PR#18072.)

Log message:
math/R: use our BLAS

This used to not actaully honour our BLAS choice, the usage of
BLAS_LIBS was missing.