---
- branch: MAIN
  date: Sat Dec 23 20:10:56 UTC 2023
  files:
  - new: '1.249'
    old: '1.248'
    path: pkgsrc/math/R/Makefile
    pathrev: pkgsrc/math/R/Makefile@1.249
    type: modified
  - new: '1.98'
    old: '1.97'
    path: pkgsrc/math/R/distinfo
    pathrev: pkgsrc/math/R/distinfo@1.98
    type: modified
  - new: '1.3'
    old: '1.2'
    path: pkgsrc/math/R/patches/patch-m4_R.m4
    pathrev: pkgsrc/math/R/patches/patch-m4_R.m4@1.3
    type: modified
  id: 20231223T201056Z.c8ad292857bb1651bc5681e5dd0b8dfd66fd215b
  log: |
    math/R: update from 4.2.0 to patch release 4.2.3 (current upstream is 4.3.2)

    Only the small update because of freeze. 4.2.0 is just outdated, 4.2.3 is from
    March this year, 4.3.2 available since end of October.

    CHANGES IN R 4.2.3:

      C-LEVEL FACILITIES:

        * The definition of DL_FUNC in R_ext/Rdynload.h has been changed to
          be fully C-compliant.  This means that functions loaded _via_ for
          example R_GetCCallable need to be cast to an appropriate type if
          they have any arguments.

        * .Machine has a new element sizeof.time_t to identify old systems
          with a 32-bit type and hence a limited range of date-times (and
          limited support for dates millions of years from present).

      PACKAGE INSTALLATION:

        * (Windows) The default C++ standard had accidentally been left at
          C++11 when it was changed to C++14 on Unix.

      BUG FIXES:

        * As "POSIXlt" objects may be "partially filled" and their list
          components meant to be recycled, length() now is the length of
          the longest component.

        * as.POSIXlt.Date() could underflow for dates in the far past (more
          than half a million years BCE).

        * as.Date.POSIXlt(x) would return "1970-01-01" instead of NA in R
          4.2.2, e.g., for

                  x <- as.POSIXlt(c("2019-01-30","2001-1-1"))
                  x$mon <- c(0L, NA); as.Date(x)

        * R CMD check failed to apply enabled _R_CHECK_SUGGESTS_ONLY_ to
          examples and vignettes (regression in R 4.2.0).

        * R CMD check did not re-build vignettes in separate processes by
          default (regression in R 4.2.0).

        * Running examples from HTML documentation now restores previous
          knitr settings and options (PR#18420).

        * Quartz: fonts are now located using Core Graphics API instead of
          deprecated ATS which is no longer supported in the macOS 13 SDK
          (PR#18426).  This also addresses an issue where the currently
          used font in the Quartz device context was not correctly
          retained.

        * (Windows) Math symbols in text drawing functions are again
          rendered correctly (PR#18440).  This fixes a regression in R
          4.2.1 caused by a fix in PR#18382 which uncovered an issue in
          GraphApp due to which the symbol charset was not used with TT
          Symbol font face.

        * (Windows) Installing a package with a src/Makefile.{win,ucrt}
          file includes ~/.R/Makevars.win64 in the search for user
          makevars, as documented in "R Installation and Administration"
          and done for packages with a src/Makevars.{win,ucrt} file.

        * format(<POSIXlt_w/_unbalanced_sec>, "....%OS<n>") with n > 0 no
          longer accidentally uses the unbalanced seconds, thanks to
          Suharto Anggono's report (including patch) in PR#18448.

        * solve.default(a, b) works around issues with some versions of
          LAPACK when a contains NA or NaN values.

        * When UseMethod() cannot dispatch, it no longer segfaults
          producing the error message in case of a long class(), thanks to
          Joris Vankerschaver's report (including patch) in PR#18447.

        * When example(foo, ..) produces graphics on an interactive device
          it needs to open itself, it now leaves devAskNewPage() unchanged
          even when it was FALSE, thus fixing a 14 years old '<FIXME>'.

        * packageDescription() again catches errors from encoding
          conversions. This also fixes broken packageVersion() in C locale
          on systems where iconv does not support transliteration.

    CHANGES IN R 4.2.2:

      NEW FEATURES:

        * tools::Rdiff(useDiff = TRUE) checks for the presence of an
          external diff command and switches to useDiff = FALSE if none is
          found.  This allows R CMD Rdiff to always work.

        * On Windows, environment variable R_LIBCURL_SSL_REVOKE_BEST_EFFORT
          can be used to switch to only 'best-effort' SSL certificate
          revocation checks with the default "libcurl" download method.
          This reduces security, but may be needed for downloads to work
          with MITM proxies (PR#18379).

        * (macOS) The run-time check for libraries from XQuartz for X11 and
          Tcl/Tk no longer uses otool from the Apple Developer Tools
          (PR#18400).

        * The LaTeX style for producing the PDF manuals, Rd.sty, now loads
          the standard amsmath, amsfonts and amssymb packages for greater
          coverage of math commands in the Rd \eqn and \deqn macros.  The
          \mathscr LaTeX command is also provided (via the mathrsfs
          package, if available, or the amsfonts bundle otherwise),
          fulfilling the wish of PR#18398.

        * (Windows) The default format of readClipboard() and
          writeClipboard() has been changed to 13 (CF_UNICODETEXT).

      INSTALLATION on a UNIX-ALIKE:

        * The PDF manuals (if built) can be compacted by the new target
          make compact-pdf (at the top level or in directory doc/manual).

        * There is now configure support for LLVM clang 15 on Linux, which
          defaults to position-independent (PIE) executables whereas
          gfortran does not.

        * Many small changes to ease compilation (and suppress warnings)
          with LLVM clang 15.

      BUG FIXES:

        * Rscript -e would fail if stdin were closed (Reported by Henrik
          Bengtsson.)

        * qt(*, log.p=TRUE) in outer tails no longer produces NaN in its
          final steps, thus fixing PR#18360.

        * tools::Rd2latex() now escapes hashes and ampersands when writing
          URLs, fixing LaTeX errors with such URLs in \tabular.

        * When isGeneric(f, fdef=*) is used with mismatching names, the
          warning is better understandable; reported (with fix) in PR#18370
          by Gabe Becker.

        * poly(x, n) now works again (and is now documented) when x is a
          "Date" or "POSIXct" object, or of another class while fulfilling
          mode(x) == "numeric".  This also enables poly(x, *, raw=TRUE) for
          such variables.  Reported by Michael Chirico to R-devel.

        * write.table(), write.csv() and write.csv2() restore their
          numerical precision (internal equivalent of digits = 15) after an
          interrupt (PR#18384).

        * One can now read also byte FF from a clipboard connection
          (PR#18385).

        * source("") and source(character()) now give more helpful error
          messages.

        * R CMD check --as-cran set _R_CHECK_TIMINGS_ too late to have the
          intended effect.

        * as.POSIXlt(x) now also works with very large dates x, fixing
          PR#18401 reported by Hannes M"uhleisen.

        * Files can now be extracted even from very large zip archives
          (PR#18390, thanks to Martin Jakt).

        * Non-finite objects of class "POSIXlt" are now correctly coerced
          to classes "Date" and "POSIXct"; following up on the extension to
          format() them correctly.

        * Added methods for is.finite(), is.infinite() and is.nan() for
          "POSIXlt" date-time objects.

      BUG FIXES on Windows:

        * Non-ASCII characters are now properly displayed on Windows in
          windows created using GraphApp via e.g. winDialogString thanks to
          a workaround for an at least surprising Windows behavior with
          UTF-8 as the system encoding (PR#18382).

        * Find and replace operations work again in the script editor in
          Rgui on Windows.

        * Computation of window size based on requested client size in
          GraphApp when running in a multi-byte locale on Windows has been
          fixed (regression in R 4.2.0 for users of systems where R 4.1
          used a single-byte locale).  Rgui again respects the number of
          console rows and columns given in Rconsole file.

        * Rterm support for Alt+xxx sequences has been fixed to produce the
          corresponding character (only) once. This fixes pasting text with
          tilde on Italian keyboard (PR#18391).

    CHANGES IN R 4.2.1:

      NEW FEATURES:

        * New function utils::findCRANmirror() to find out if a CRAN mirror
          has been selected, otherwise fallback to the main site.  This
          behaves in the same way as tools::CRAN_package_db() and is
          intended for packages wishing to access CRAN for purposes other
          than installing packages.

          The need for this was shown by a day when the main CRAN website
          was offline and a dozen or so packages which had its URL
          hardcoded failed their checks.

      INSTALLATION on a UNIX-ALIKE:

        * The libraries searched for by --with-blas (without a value) now
          include BLIS (after OpenBLAS but before ATLAS).  And on macOS,
          the Accelerate framework (after ATLAS).  (This is patterned after
          the AX_BLAS macro from the Autoconf Archive.)

        * The included LAPACK sources have been updated to 3.10.1.

      UTILITIES:

        * The (full path to) the command tidy to be used for HTML
          validation can be set by environment variable R_TIDYCMD.

        * Setting environment variable _R_CHECK_RD_VALIDATE_RD2HTML_ to a
          false value will override R CMD check --as-cran and turn off HTML
          validation.  This provides a way to circumvent a problematic
          tidy.

          The 2006 version that ships with macOS is always skipped.

      C-LEVEL FACILITIES:

        * The undocumented legacy declarations of Sint, Sfloat, SINT_MAX
          and SINT_MIN in header R.h are deprecated.

      BUG FIXES:

        * fisher.test(d) no longer segfaults for "large" d; fixing PR#18336
          by preventing/detecting an integer overflow reliably.

        * tar(., files=*) now produces correctly the warning about invalid
          UID or GID of files, fixing PR#18344, reported by Martin Morgan.

        * tk_choose.files() with multi = FALSE misbehaved on paths
          containing spaces (PR#18334) (regression introduced in R 4.0.0).

        * sort(x, partial = ind, *) now works correctly notably for the
          non-default na.last = FALSE or TRUE, fixing PR#18335 reported by
          James Edwards.

        * Environment variable _R_CHECK_XREFS_REPOSITORIES_ is only used
          for checking .Rd cross-references in R CMD check (as documented)
          and not for other uses looking for a CRAN mirror.

        * The search for a CRAN mirror when checking packages now uses
          getOption("repos") if that specifies a CRAN mirror, even when it
          does not also specify all three Bioconductor repositories (as was
          previously required).

        * The HTML code generated by tools::Rd2HTML() has been improved to
          pass tidy 5.8.0.

      BUG FIXES on Windows:

        * Writing to a clipboard connection works again, fixing a
          regression in R 4.2.0 (PR#18332).  Re-using a closed clipboard
          connection no longer issues a spurious warning about an ignored
          encoding argument.

        * C function getlocale no longer attempts to query an unsupported
          category from the OS, even when requested at R level, which may
          cause crashes when R 4.2.0 (which uses UCRT) is embedded
          (reported by Kevin Ushey).

        * Accent keys now work in GraphApp Unicode windows, which are used
          by Rgui whenever running in a multibyte locale (so also in UTF-8,
          hence fixing a regression in R 4.2.0 for users of systems where R
          4.1 used a single-byte locale).

        * Completion in Rgui now works also with non-ASCII characters.

        * Rgui no longer truncates usage information with --help.

        * Text injection from external applications via SendInput now works
          in GraphApp Unicode windows, fixing a regression in R 4.2.0 for
          Rgui users of systems where R 4.1 used a single-byte locale but R
          4.2.0 uses UTF-8.

        * Performance of txtProgressBar() in Rgui when running in a
          multi-byte locale has been improved (fixing a performance
          regression in R 4.2.0 for users of systems where R 4.1 used a
          single-byte locale).

        * The script editor in Rgui now works also on systems using UTF-8
          as the native encoding.  Users of the script editor have to
          convert their scripts with non-ASCII characters to UTF-8 before
          reading them in R 4.2.1 or newer (on recent Windows where UTF-8
          is used).  This fixes a regression in R 4.2.0, which prevented
          some operations with scripts when they contained non-ASCII
          characters.
  module: pkgsrc
  subject: 'CVS commit: pkgsrc/math/R'
  unixtime: '1703362256'
  user: thor