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(math/R) updated 4.5.3 to 4.6.0

Module Name:	pkgsrc-wip
Committed By:	Makoto Fujiwara <makoto%if.t.u-tokyo.ac.jp@localhost>
Pushed By:	mef
Date:		Thu May 14 06:59:56 2026 +0900
Changeset:	e09f6d186725897dc1f5e98ec6186c8d386fff44

Modified Files:
	R/Makefile
	R/PLIST
	R/distinfo
	R/patches/patch-configure.ac

Log Message:
(math/R) updated 4.5.3 to 4.6.0

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e09f6d186725897dc1f5e98ec6186c8d386fff44

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

diffstat:
 R/Makefile                   |  3 ++-
 R/PLIST                      | 35 +++++++++++++++++++++++++++++------
 R/distinfo                   |  8 ++++----
 R/patches/patch-configure.ac | 23 ++++++++++++++++-------
 4 files changed, 51 insertions(+), 18 deletions(-)

diffs:
diff --git a/R/Makefile b/R/Makefile
index 964940343b..d152463468 100644
--- a/R/Makefile
+++ b/R/Makefile
@@ -4,9 +4,10 @@
 # If updating this package, please try to ensure PLIST.Darwin is kept in sync
 # to avoid unnecessarily breaking macOS users.
 #
-DISTNAME=	R-4.5.3
+DISTNAME=	R-4.6.0
 CATEGORIES=	math
 MASTER_SITES=	${MASTER_SITE_R_CRAN:=base/R-4/}
+EXTRACT_SUFX=	.tar.xz
 
 MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
 HOMEPAGE=	https://www.R-project.org/
diff --git a/R/PLIST b/R/PLIST
index 61da1dcde7..d006b78f35 100644
--- a/R/PLIST
+++ b/R/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.45 2026/03/12 11:22:57 mef Exp $
+@comment $NetBSD$
 bin/R
 bin/Rscript
 info/R-FAQ.info.gz
@@ -179,9 +179,9 @@ lib/R/include/R_ext/Lapack.h
 lib/R/include/R_ext/Linpack.h
 lib/R/include/R_ext/MathThreads.h
 lib/R/include/R_ext/Memory.h
+lib/R/include/R_ext/ObjectTable.h
 lib/R/include/R_ext/Parse.h
 lib/R/include/R_ext/Print.h
-lib/R/include/R_ext/PrtUtil.h
 lib/R/include/R_ext/QuartzDevice.h
 lib/R/include/R_ext/RS.h
 lib/R/include/R_ext/RStartup.h
@@ -229,7 +229,6 @@ lib/R/library/KernSmooth/po/fr/LC_MESSAGES/R-KernSmooth.mo
 lib/R/library/KernSmooth/po/it/LC_MESSAGES/R-KernSmooth.mo
 lib/R/library/KernSmooth/po/ko/LC_MESSAGES/R-KernSmooth.mo
 lib/R/library/KernSmooth/po/pl/LC_MESSAGES/R-KernSmooth.mo
-lib/R/library/lattice/help/figures/logo.svg
 lib/R/library/MASS/CITATION
 lib/R/library/MASS/DESCRIPTION
 lib/R/library/MASS/INDEX
@@ -858,6 +857,7 @@ lib/R/library/lattice/NEWS.md
 lib/R/library/lattice/R/lattice
 lib/R/library/lattice/R/lattice.rdb
 lib/R/library/lattice/R/lattice.rdx
+lib/R/library/lattice/README.md
 lib/R/library/lattice/data/Rdata.rdb
 lib/R/library/lattice/data/Rdata.rds
 lib/R/library/lattice/data/Rdata.rdx
@@ -871,6 +871,7 @@ lib/R/library/lattice/doc/grid.pdf
 lib/R/library/lattice/doc/index.html
 lib/R/library/lattice/help/AnIndex
 lib/R/library/lattice/help/aliases.rds
+lib/R/library/lattice/help/figures/logo.svg
 lib/R/library/lattice/help/lattice.rdb
 lib/R/library/lattice/help/lattice.rdx
 lib/R/library/lattice/help/paths.rds
@@ -1048,6 +1049,7 @@ lib/R/library/rpart/NEWS.Rd
 lib/R/library/rpart/R/rpart
 lib/R/library/rpart/R/rpart.rdb
 lib/R/library/rpart/R/rpart.rdx
+lib/R/library/rpart/README.md
 lib/R/library/rpart/data/Rdata.rdb
 lib/R/library/rpart/data/Rdata.rds
 lib/R/library/rpart/data/Rdata.rdx
@@ -1331,7 +1333,8 @@ lib/R/library/tools/help/tools.rdx
 lib/R/library/tools/html/00Index.html
 lib/R/library/tools/html/R.css
 lib/R/library/tools/libs/tools.so
-lib/R/library/tools/wre.txt
+lib/R/library/tools/misc/top.txt
+lib/R/library/tools/misc/wre.txt
 lib/R/library/translations/DESCRIPTION
 lib/R/library/translations/ar/LC_MESSAGES/R-base.mo
 lib/R/library/translations/ar/LC_MESSAGES/R-methods.mo
@@ -1833,6 +1836,9 @@ lib/R/library/utils/R/utils.rdb
 lib/R/library/utils/R/utils.rdx
 lib/R/library/utils/Sweave/Sweave-test-1.Rnw
 lib/R/library/utils/Sweave/example-1.Rnw
+lib/R/library/utils/Sweave/example-2.Rnw
+lib/R/library/utils/Sweave/example-3.Rnw
+lib/R/library/utils/Sweave/example-4.Rnw
 lib/R/library/utils/doc/Sweave.pdf
 lib/R/library/utils/help/AnIndex
 lib/R/library/utils/help/aliases.rds
@@ -1845,8 +1851,8 @@ lib/R/library/utils/iconvlist
 lib/R/library/utils/libs/utils.so
 lib/R/library/utils/misc/exDIF.csv
 lib/R/library/utils/misc/exDIF.dif
-${PLIST.x11}lib/R/modules/R_X11.so
-${PLIST.x11}lib/R/modules/R_de.so
+lib/R/modules/R_X11.so
+lib/R/modules/R_de.so
 lib/R/modules/internet.so
 lib/R/modules/lapack.so
 lib/R/share/R/REMOVE.R
@@ -1855,18 +1861,35 @@ lib/R/share/R/examples-header.R
 lib/R/share/R/nspackloader.R
 lib/R/share/R/tests-startup.R
 lib/R/share/Rd/macros/system.Rd
+lib/R/share/bibliographies/R.rds
+lib/R/share/bibliographies/base.R
+lib/R/share/bibliographies/datasets.R
+lib/R/share/bibliographies/grDevices.R
+lib/R/share/bibliographies/graphics.R
+lib/R/share/bibliographies/grid.R
+lib/R/share/bibliographies/methods.R
+lib/R/share/bibliographies/parallel.R
+lib/R/share/bibliographies/splines.R
+lib/R/share/bibliographies/stats.R
+lib/R/share/bibliographies/utils.R
 lib/R/share/dictionaries/R_Rd_files.rds
+lib/R/share/dictionaries/R_Rd_files.txt
 lib/R/share/dictionaries/R_manuals.rds
+lib/R/share/dictionaries/R_manuals.txt
 lib/R/share/dictionaries/R_vignettes.rds
+lib/R/share/dictionaries/R_vignettes.txt
 lib/R/share/dictionaries/en_stats.rds
+lib/R/share/dictionaries/en_stats.txt
 lib/R/share/encodings/Adobe-glyphlist
 lib/R/share/encodings/character-sets
 lib/R/share/java/README
 lib/R/share/java/getsp.class
 lib/R/share/licenses/AGPL-3
+lib/R/share/licenses/Apache-2.0
 lib/R/share/licenses/Artistic-2.0
 lib/R/share/licenses/BSD_2_clause
 lib/R/share/licenses/BSD_3_clause
+lib/R/share/licenses/CC0-1.0
 lib/R/share/licenses/GPL-2
 lib/R/share/licenses/GPL-3
 lib/R/share/licenses/LGPL-2
diff --git a/R/distinfo b/R/distinfo
index 4d2438016e..4d024523eb 100644
--- a/R/distinfo
+++ b/R/distinfo
@@ -1,9 +1,9 @@
 $NetBSD: distinfo,v 1.116 2026/04/14 10:33:41 jperkin Exp $
 
-BLAKE2s (R-4.5.3.tar.gz) = 587e35a109716f1521c896d772b19d5d3af06c4ea82c3a0e45af2c49fd52bc89
-SHA512 (R-4.5.3.tar.gz) = 9481ba6a8584954954d754116d45cbaec4f7003e2f1b1b450b05df6487e0f87950949e20c6a6805e5429b55a0f00208c1c1ef9a05fa3cc8c8d220fe9963cc56b
-Size (R-4.5.3.tar.gz) = 40518619 bytes
-SHA1 (patch-configure.ac) = 17caa1621e93a04be23fc037805fd7240a52d17b
+BLAKE2s (R-4.6.0.tar.xz) = d51fbdc7b1c102086e9395971f6b2a2fc03fc6d9588da35cad810ef56f8e4ea5
+SHA512 (R-4.6.0.tar.xz) = d891378209298169781d7a785bc959aabf6cb79754e2d303245ce87fa5f1b5c77817a365a6adf4bc64d283bb72a4d774811332ee80638cae2390649bb2934b37
+Size (R-4.6.0.tar.xz) = 30948604 bytes
+SHA1 (patch-configure.ac) = 595d6447cc794aec12843bb37e7857d681f58bc1
 SHA1 (patch-src_extra_xdr_xdr__mem.c) = 2e607b070db8b24a6ad5501e9c7c1549bf1b1d82
 SHA1 (patch-src_extra_xdr_xdr__stdio.c) = 91ea16599693e9dc14e631880fbe1c52f0f2009f
 SHA1 (patch-src_include_R__ext_Error.h) = 2d1eaebff5e57d73d301f7e818daa0b959a5c0f2
diff --git a/R/patches/patch-configure.ac b/R/patches/patch-configure.ac
index 05916ccb2d..dd825f6211 100644
--- a/R/patches/patch-configure.ac
+++ b/R/patches/patch-configure.ac
@@ -25,9 +25,9 @@ release    line #
 10.99.12   4770   withval=$with_blas; if test "${withval}" = no; then
  9.3       4392   withval=$with_blas; R_ARG_USE(blas)
 
---- configure.ac.orig	2025-04-20 22:15:02.000000000 +0000
-+++ configure.ac
-@@ -33,6 +33,7 @@ m4_define([R_VERSION],
+--- configure.ac.orig	2026-03-27 08:02:02.000000000 +0900
++++ configure.ac	2026-05-14 00:06:25.314689723 +0900
+@@ -33,6 +33,7 @@
  AC_INIT([R],[R_VERSION],[https://bugs.r-project.org],[R],[https://www.r-project.org])
  AC_CONFIG_SRCDIR([src/include/Defn.h])
  AC_CONFIG_AUX_DIR([tools])
@@ -35,7 +35,7 @@ release    line #
  
  ### * Information on the package.
  
-@@ -322,6 +323,8 @@ AC_ARG_ENABLE([BLAS-shlib],
+@@ -328,6 +329,8 @@
  ## As from R 3.2.0 split up -L... and -lR
  if test "${want_R_shlib}" = yes; then
    LIBR0="-L\"\$(R_HOME)/lib\$(R_ARCH)\""
@@ -44,7 +44,7 @@ release    line #
    LIBR1=-lR
  else
    LIBR0=
-@@ -936,7 +939,7 @@ case "${host_os}" in
+@@ -942,7 +945,7 @@
      ## Not so bad in later versions of Darwin, 
      ## where DYLD_FALLBACK_LIBRARY_PATH is used (see below).
      ;;
@@ -53,7 +53,7 @@ release    line #
      for arg in ${LDFLAGS}; do
        case "${arg}" in
          -L*)
-@@ -1864,8 +1867,8 @@ dnl     ;;
+@@ -1874,8 +1877,8 @@
      DYLIB_EXT=".dylib"
      dylib_ldflags="${darwin_dylib_ldflags}"
      MAJR_VERSION=`echo "${PACKAGE_VERSION}" | sed  -e "s/[[\.]][[1-9]]$/.0/"` 
@@ -64,7 +64,16 @@ release    line #
      ## don't use version in libRblas so we can replace it with any BLAS implementation
      RBLAS_LDFLAGS="-install_name libRblas.dylib -headerpad_max_install_names"
      ;;
-@@ -2895,7 +2898,7 @@ for arg in ${LDFLAGS} ${FLIBS} ${BLAS_LI
+@@ -1961,7 +1964,7 @@
+   use_CXX20=no
+ fi
+ if test -n "${CXX}" && test -z "${CXXSTD}"; then
+-  if test "$use_CXX20" == "yes"; then
++  if test "$use_CXX20" = "yes"; then
+ dnl Set default C++ compiler to C++20 as available
+     CXX=${CXX20}
+     CXXSTD=${CXX20STD}
+@@ -2912,7 +2915,7 @@
    case "${arg}" in
      -L*)
        lib=`echo ${arg} | sed "s/^-L//"`
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