[pkgsrc/trunk]: pkgsrc/math/R Update to 4.1.2

[wen <wen%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/efae5769a3d9
branches:  trunk
changeset: 768944:efae5769a3d9
user:      wen <wen%pkgsrc.org@localhost>
date:      Thu Nov 04 14:38:47 2021 +0000

description:
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).

diffstat:

 math/R/Makefile |  5 ++---
 math/R/PLIST    |  5 ++++-
 math/R/distinfo |  8 ++++----
 3 files changed, 10 insertions(+), 8 deletions(-)

diffs (48 lines):

diff -r 5603041b086e -r efae5769a3d9 math/R/Makefile
--- a/math/R/Makefile   Thu Nov 04 13:56:55 2021 +0000
+++ b/math/R/Makefile   Thu Nov 04 14:38:47 2021 +0000
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.226 2021/09/29 19:00:56 adam Exp $
+# $NetBSD: Makefile,v 1.227 2021/11/04 14:38:47 wen Exp $
 
-DISTNAME=      R-4.1.1
-PKGREVISION=   1
+DISTNAME=      R-4.1.2
 CATEGORIES=    math
 MASTER_SITES=  ${MASTER_SITE_R_CRAN:=base/R-4/}
 
diff -r 5603041b086e -r efae5769a3d9 math/R/PLIST
--- a/math/R/PLIST      Thu Nov 04 13:56:55 2021 +0000
+++ b/math/R/PLIST      Thu Nov 04 14:38:47 2021 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.34 2021/06/13 13:10:46 wen Exp $
+@comment $NetBSD: PLIST,v 1.35 2021/11/04 14:38:47 wen Exp $
 bin/R
 bin/Rscript
 info/R-FAQ.info.gz
@@ -1107,6 +1107,9 @@
 lib/R/library/survival/doc/concordance.R
 lib/R/library/survival/doc/concordance.Rnw
 lib/R/library/survival/doc/concordance.pdf
+lib/R/library/survival/doc/discrim.R
+lib/R/library/survival/doc/discrim.Rnw
+lib/R/library/survival/doc/discrim.pdf
 lib/R/library/survival/doc/index.html
 lib/R/library/survival/doc/multi.Rnw
 lib/R/library/survival/doc/multi.pdf
diff -r 5603041b086e -r efae5769a3d9 math/R/distinfo
--- a/math/R/distinfo   Thu Nov 04 13:56:55 2021 +0000
+++ b/math/R/distinfo   Thu Nov 04 14:38:47 2021 +0000
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.91 2021/10/26 10:55:21 nia Exp $
+$NetBSD: distinfo,v 1.92 2021/11/04 14:38:47 wen Exp $
 
-BLAKE2s (R-4.1.1.tar.gz) = bb8c39ee46c3220929f964d81b2422486b750e0187815aedafeaee1e48eb313e
-SHA512 (R-4.1.1.tar.gz) = 8eef82c0321f53a6a737bb641c4401626682fd01fa21e497ed2b8d6291d94ada47cee46b258bb3052f1097fc087c72982b2625c80420c8fb230ba8fcd962f254
-Size (R-4.1.1.tar.gz) = 33719965 bytes
+BLAKE2s (R-4.1.2.tar.gz) = 8ef0d0b0599eca38ff309edda9df7098476335a52d5f6e363b97855044414228
+SHA512 (R-4.1.2.tar.gz) = 657c7950a88f632f1bbb08dbd0b3fb485732a25d8bbcb8a7939a40b23c7a235fdb9b46c296acaa9f72eabebe96e270ecbdcd7970fc9d3a299e6687bea45f2d3f
+Size (R-4.1.2.tar.gz) = 34009074 bytes
 SHA1 (patch-configure.ac) = 2732e3e0a39ee64ae4cba5c476f4754ecbd14942
 SHA1 (patch-m4_R.m4) = 704d5514e10adf0b5217bb71b06f44a612eca6e0
 SHA1 (patch-src_library_stats_src_Makefile.in) = 4eb93292858392792c37a706399e2cef91821bbe