[pkgsrc/trunk]: pkgsrc/math/R Update to 4.1.1

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

details:   https://anonhg.NetBSD.org/pkgsrc/rev/60fe6e061098
branches:  trunk
changeset: 456900:60fe6e061098
user:      wen <wen%pkgsrc.org@localhost>
date:      Wed Aug 11 09:38:37 2021 +0000

description:
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.)

diffstat:

 math/R/Makefile                            |   5 ++---
 math/R/distinfo                            |  10 +++++-----
 math/R/patches/patch-src_main_printutils.c |  13 -------------
 3 files changed, 7 insertions(+), 21 deletions(-)

diffs (48 lines):

diff -r 62fa02b92bf3 -r 60fe6e061098 math/R/Makefile
--- a/math/R/Makefile   Wed Aug 11 07:56:31 2021 +0000
+++ b/math/R/Makefile   Wed Aug 11 09:38:37 2021 +0000
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.224 2021/06/15 06:51:42 thor Exp $
+# $NetBSD: Makefile,v 1.225 2021/08/11 09:38:37 wen Exp $
 
-DISTNAME=      R-4.1.0
-PKGREVISION=   1
+DISTNAME=      R-4.1.1
 CATEGORIES=    math
 MASTER_SITES=  ${MASTER_SITE_R_CRAN:=base/R-4/}
 
diff -r 62fa02b92bf3 -r 60fe6e061098 math/R/distinfo
--- a/math/R/distinfo   Wed Aug 11 07:56:31 2021 +0000
+++ b/math/R/distinfo   Wed Aug 11 09:38:37 2021 +0000
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.88 2021/06/13 13:10:46 wen Exp $
+$NetBSD: distinfo,v 1.89 2021/08/11 09:38:37 wen Exp $
 
-SHA1 (R-4.1.0.tar.gz) = c84697f2a0a5b89ff75dfe10fcb87656cc68144c
-RMD160 (R-4.1.0.tar.gz) = fe7de80b43c678ed20fada00b4cad89d8df56d10
-SHA512 (R-4.1.0.tar.gz) = 41519bf06a1ebc2bb582e9a7c35d0e82e213312dec8147861a7f9b28ee750cd40dfbf02737602d05698641fcea6182b0da8131e83edacc358e98eca0a393b729
-Size (R-4.1.0.tar.gz) = 33714683 bytes
+SHA1 (R-4.1.1.tar.gz) = a7c40a9bd7cb050a4fad6b7dba53e991e37e0fd1
+RMD160 (R-4.1.1.tar.gz) = d0eb885bb3f3da858e023b2983098e927af70aaa
+SHA512 (R-4.1.1.tar.gz) = 8eef82c0321f53a6a737bb641c4401626682fd01fa21e497ed2b8d6291d94ada47cee46b258bb3052f1097fc087c72982b2625c80420c8fb230ba8fcd962f254
+Size (R-4.1.1.tar.gz) = 33719965 bytes
 SHA1 (patch-configure.ac) = 2732e3e0a39ee64ae4cba5c476f4754ecbd14942
 SHA1 (patch-m4_R.m4) = 704d5514e10adf0b5217bb71b06f44a612eca6e0
 SHA1 (patch-src_library_stats_src_Makefile.in) = 4eb93292858392792c37a706399e2cef91821bbe
diff -r 62fa02b92bf3 -r 60fe6e061098 math/R/patches/patch-src_main_printutils.c
--- a/math/R/patches/patch-src_main_printutils.c        Wed Aug 11 07:56:31 2021 +0000
+++ /dev/null   Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-$NetBSD: patch-src_main_printutils.c,v 1.1 2021/06/13 13:10:47 wen Exp $
-
---- src/main/printutils.c.orig 2021-04-19 22:02:06.000000000 +0000
-+++ src/main/printutils.c
-@@ -752,7 +752,7 @@ const char *EncodeString(SEXP s, int w, 
-                       for(int j = 0; j < res; j++) *q++ = *p++;
-                   } else {
- # if !defined (__STDC_ISO_10646__) && !defined (Win32)
--                      if(!use_ucs) Unicode_warning = TRUE;
-+                      Unicode_warning = TRUE;
- # endif
-                       if(k > 0xffff)
-                           snprintf(buf, 13, "\\U{%06x}", k);