CVS commit: pkgsrc/math/R

["Dr. Thomas Orgis" <thor%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   thor
Date:           Sat Dec 23 20:10:56 UTC 2023

Modified Files:
        pkgsrc/math/R: Makefile distinfo
        pkgsrc/math/R/patches: patch-m4_R.m4

Log Message:
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Only the small update because of freeze. 4.2.0 is just outdated, 4.2.3 is from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.


To generate a diff of this commit:
cvs rdiff -u -r1.248 -r1.249 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.97 -r1.98 pkgsrc/math/R/distinfo
cvs rdiff -u -r1.2 -r1.3 pkgsrc/math/R/patches/patch-m4_R.m4

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/R/Makefile
diff -u pkgsrc/math/R/Makefile:1.248 pkgsrc/math/R/Makefile:1.249
--- pkgsrc/math/R/Makefile:1.248        Tue Nov 14 14:02:26 2023
+++ pkgsrc/math/R/Makefile      Sat Dec 23 20:10:56 2023
@@ -1,11 +1,10 @@
-# $NetBSD: Makefile,v 1.248 2023/11/14 14:02:26 wiz Exp $
+# $NetBSD: Makefile,v 1.249 2023/12/23 20:10:56 thor Exp $
 
 #
 # If updating this package, please try to ensure PLIST.Darwin is kept in sync
 # to avoid unnecessarily breaking macOS users.
 #
-DISTNAME=      R-4.2.0
-PKGREVISION=   12
+DISTNAME=      R-4.2.3
 CATEGORIES=    math
 MASTER_SITES=  ${MASTER_SITE_R_CRAN:=base/R-4/}
 

Index: pkgsrc/math/R/distinfo
diff -u pkgsrc/math/R/distinfo:1.97 pkgsrc/math/R/distinfo:1.98
--- pkgsrc/math/R/distinfo:1.97 Wed Mar 22 13:53:29 2023
+++ pkgsrc/math/R/distinfo      Sat Dec 23 20:10:56 2023
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.97 2023/03/22 13:53:29 wiz Exp $
+$NetBSD: distinfo,v 1.98 2023/12/23 20:10:56 thor Exp $
 
-BLAKE2s (R-4.2.0.tar.gz) = 387280cfca2ea0ed9963f4a9ed4f8cd1a2a81fc9235808659dd22a516e5ddd22
-SHA512 (R-4.2.0.tar.gz) = 99e71dad00b63e44bfcb8dc9539ff1951809112882d9ee7e06a4e99bce2e6ceac24e8348fd598c21e6d5ab0e0629a85170cde208bfa8145af91c398ac4ef7bcd
-Size (R-4.2.0.tar.gz) = 37585694 bytes
+BLAKE2s (R-4.2.3.tar.gz) = 68ba598f6aec52d4464bb9c4bca99398af63d31257f1bff95d8aeb0547e9dbc8
+SHA512 (R-4.2.3.tar.gz) = 060bb4e1d1f1a5a0383a3b4372ac9247c0a20285020da17cebeb40ddc54da12d5f369ea243ea04d2c6970986fe22b3f9c37fbdfb3405cd8aa4f2353091ea9c5c
+Size (R-4.2.3.tar.gz) = 34010655 bytes
 SHA1 (patch-configure.ac) = d6661984716a131bbfa1a2aa56385c535881d43d
-SHA1 (patch-m4_R.m4) = c55ae5a10bb995e147aceb12fd7393d8a6a64876
+SHA1 (patch-m4_R.m4) = f21948d2c1f662611e0bca3922dc2dedeabd473e
 SHA1 (patch-src_library_stats_src_Makefile.in) = 4eb93292858392792c37a706399e2cef91821bbe
 SHA1 (patch-src_main_character.c) = 842ae5d291f36f2beead4d32c1d41b18cbff878d

Index: pkgsrc/math/R/patches/patch-m4_R.m4
diff -u pkgsrc/math/R/patches/patch-m4_R.m4:1.2 pkgsrc/math/R/patches/patch-m4_R.m4:1.3
--- pkgsrc/math/R/patches/patch-m4_R.m4:1.2     Wed Mar 22 13:53:29 2023
+++ pkgsrc/math/R/patches/patch-m4_R.m4 Sat Dec 23 20:10:56 2023
@@ -1,8 +1,8 @@
-$NetBSD: patch-m4_R.m4,v 1.2 2023/03/22 13:53:29 wiz Exp $
+$NetBSD: patch-m4_R.m4,v 1.3 2023/12/23 20:10:56 thor Exp $
 
 Ensure tests for clog & co. fail, not just emit warning
 
---- m4/R.m4.orig       2022-04-03 22:15:01.000000000 +0000
+--- m4/R.m4.orig       2022-11-01 23:15:01.000000000 +0000
 +++ m4/R.m4
 @@ -225,7 +225,7 @@ if test -z "${texi2any_version_maj}" \
  elif test ${texi2any_version_maj} -gt 5; then
@@ -33,7 +33,7 @@ Ensure tests for clog & co. fail, not ju
  int main () {
      Rcomplex z[3];
  
-@@ -3733,9 +3739,9 @@ R_CHECK_FUNCS([cabs carg cexp clog csqrt
+@@ -3763,9 +3769,9 @@ R_CHECK_FUNCS([cabs carg cexp clog csqrt
  AC_DEFUN([R_CHECK_DECL],
  [AS_VAR_PUSHDEF([ac_Symbol], [ac_cv_have_decl_$1])dnl
  AC_CACHE_CHECK([whether $1 exists and is declared], ac_Symbol,
@@ -46,8 +46,8 @@ Ensure tests for clog & co. fail, not ju
  #endif
  ])],
                     [AS_VAR_SET(ac_Symbol, yes)],
-@@ -4277,9 +4283,9 @@ AC_CACHE_CHECK([if libcurl is version 7 
- int main() 
+@@ -4307,9 +4313,9 @@ AC_CACHE_CHECK([if libcurl is version 7
+ int main(int argc, const char * argv[]) 
  {
  #ifdef LIBCURL_VERSION_MAJOR
 -#if LIBCURL_VERSION_MAJOR > 7