(math/R) Updated 4.6.0 to 4.6.1, build clang is now OK

[Makoto Fujiwara (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Makoto Fujiwara <makoto%if.t.u-tokyo.ac.jp@localhost>
Pushed By:	mef
Date:		Sat Jun 27 17:00:53 2026 +0900
Changeset:	25fc511cabba217a77d8540e4e4bead1dba9ff37

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

Log Message:
(math/R) Updated 4.6.0 to 4.6.1, build clang is now OK

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=25fc511cabba217a77d8540e4e4bead1dba9ff37

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

diffstat:
 R/COMMIT_MSG                 | 102 ++++++++++++++++++++-----------------------
 R/Makefile                   |   7 +--
 R/PLIST                      |   4 +-
 R/distinfo                   |   8 ++--
 R/patches/patch-configure.ac |  16 +++----
 5 files changed, 66 insertions(+), 71 deletions(-)

diffs:
diff --git a/R/COMMIT_MSG b/R/COMMIT_MSG
index e127090305..50149b8551 100644
--- a/R/COMMIT_MSG
+++ b/R/COMMIT_MSG
@@ -1,70 +1,64 @@
-(math/R) Updated 4.5.2 to 4.5.3
+(math/R) Updated 4.6.0 to 4.6.1, build with clang is Now OK
 
-CHANGES IN R 4.5.3:
+Changes in R 4.6.1:
 
-  UTILITIES:
+  New Features:
 
-    * tools/fetch-recommended can be used instead of
-      tools/rsync-recommended to fetch recommended packages into R
-      sources using curl on systems without rsync or behind firewalls.
+         * The LaTeX class 'jss' bundled in
+           'share/texmf/tex/latex/jss.cls' has been updated to work
+           with 'hyperref' version 7.01q (2026/04/24).
 
-  PACKAGE INSTALLATION:
+         * Plain-text (and legacy HTML) conversion for a simple Rd
+           \eqn{} now handles \geq, \leq, \neq and \ne in addition to
+           \ge and \le (PR#19070).
 
-    * C++ standard specifications (CXX_STD = in src/Makevars* and in
-      the SystemRequirements field of the DESCRIPTION file) are now
-      checked more thoroughly.  Invalid values are still ignored but
-      now give a warning, as do contradictory specifications.
+  Bug Fixes:
 
-    * (Preliminary) support for C++26 has been extended to Windows.
+         * 'abbreviate(<non-ASCII>)' now works better, using
+           'iswlower()' and '*upper()' to treat "wide" characters,
+           thanks to Kevin's PR#19058.
 
-    * A non-zero exit status from cleanup, cleanup.win or cleanup.ucrt,
-      if requested via options --clean or --preclean, is now reported
-      with a warning.
+         * 'cut(1:11, {})' now signals an error for the invalid
+           'breaks', fixing PR#19057, thanks to Kevin Ushey.
 
-  BUG FIXES:
+         * 'all(<symbol>)' signals an error now, as some similar
+           coercions; previously, the coercion of the symbol resulted
+           in 'NULL' internally, raised a warning, and could access
+           illegal memory; thanks to Kevin Ushey's PR#19054.
 
-    * all.equal(obj, simple, check.class=FALSE) now is true, also when
-      simple is a bare atomic vector and obj has a simple class, fixing
-      the first part of PR#18971 thanks to Jan Gorecki.
+         * 'stl()' now checks its 3 x 3 tuning parameters on the R
+           level; 'stl(*, s.window = 0)' now "works" instead dumping
+           core, 'stl(*, s.window = 1)' "works" correctly, too.  Also,
+           the 'summary()' method mentions the robustness 'weights'
+           only if any robustness iterations happened.
 
-    * str(x, give.attr=FALSE) no longer shows attributes when x is a
-      zero length "Date" or "POSIXt" object.
+           Further, 'stl()' is now based on C code, translated from
+           previous Fortran, triggered by a flang 22 compiler
+           optimization bug ('-O2').
 
-    * Tweaks to binning for bw.SJ() and bw.ucv() in the very rare case
-      of data which have an extremely small range compared to their
-      absolute values, e.g., x <- 6e9 + 6:9.
+         * The border case 'zapsmall(x, digits=Inf)' where 'x' contains
+           an 'Inf' entry no longer returns all 'NaN' but rather 'x'.
+           The improved help page now has more non-default examples.
 
-    * Formatting book-type bibentry objects now converts LaTeX accents
-      also in the publisher and series fields.
+         * 'wilcox.test(x, exact=FALSE, correct = k)''s p-value
+           computation got a missing 'dnorm(z)' factor, and so did the
+           2-sample case, in addition to more fixes.
 
-    * model.frame(~1, list(), na.action=na.pass) and similar
-      "border-line" uses no longer produce invalid data frames, fixing
-      PR#18977, reported with patch by Mikael Jagan.
+         * The data part of 'getGenerics()' listed package names for
+           generic functions defined in more than one package.  Now it
+           lists generic function names, as intended.  Thanks to
+           Michael Chirico for report and patch proposal (PR#19080).
 
-    * length(<POSIXlt>) <- v is more careful about balancing, notably
-      when v is not integer, thanks to Suharto Anggono's remarks on the
-      mailing list R-devel.
+         * Overly long 'dyn.load()' error messages (C level
+           'dlerror()'), should no longer corrupt its state, thanks to
+           Ivan Krylov's PR#19029 report and patch.
 
-    * approx(<x_with_ties>, <y_with_NA>, na.rm = FALSE) now should
-      always call the ties() function, fixing PR#17604 reported by Bill
-      Dunlap.
+         * 'as.matrix(<POSIXlt>)' again produces a _numeric_ matrix,
+           and the 'c()' and subassignment methods for 'POSIXlt'
+           objects work correctly more often, e.g., without a '"tzone"'
+           attribute, back porting a few of the PR#18989 fixes from
+           R-devel, both thanks to Suharto Anggono.
 
-    * besselJ(1, 1e-15) and similar now give correct results, thanks to
-      Leo Mada and other "R-help"ers.
-
-    * vignette(<pkg>::<topic>) is now a documented usage variant and
-      confines vignette retrieval to the specified package.
-
-    * pretty(ch) again correctly works with ch a character vector of
-      numbers.
-
-    * persp() labels the three axes correctly also when C level
-      atan2pi() is available, fixing PR#19007 by Klaus Schliep.
-
-    * Large (tall) subscripts in plotmath expressions are now
-      positioned correctly.  They were being positioned too high.
-
-    * Ops group (Arith, Compare,..) methods for matrix-"ts" now do
-      return (zero length) matrices even when the two series do not
-      overlap, a very partial fix of PR#18972 which is to be fully
-      addressed later.
+         * In 'methods', 'as()' now correctly coerces S4 objects to S4
+           superclasses extending old-style classes, instead of
+           returning only the S3 part.
diff --git a/R/Makefile b/R/Makefile
index d152463468..e5a0b16efd 100644
--- a/R/Makefile
+++ b/R/Makefile
@@ -4,7 +4,7 @@
 # If updating this package, please try to ensure PLIST.Darwin is kept in sync
 # to avoid unnecessarily breaking macOS users.
 #
-DISTNAME=	R-4.6.0
+DISTNAME=	R-4.6.1
 CATEGORIES=	math
 MASTER_SITES=	${MASTER_SITE_R_CRAN:=base/R-4/}
 EXTRACT_SUFX=	.tar.xz
@@ -38,6 +38,7 @@ PTHREAD_AUTO_VARS=	yes
 
 GNU_CONFIGURE=		yes
 GNU_CONFIGURE_ICONV=	no
+CONFIGURE_ARGS+=	--disable-java
 CONFIGURE_ARGS+=	--enable-R-shlib
 CONFIGURE_ARGS+=	--with-readline
 CONFIGURE_ARGS+=	--with-tcltk
@@ -55,8 +56,8 @@ CONFIGURE_ARGS+=	--enable-long-double=no
 CONFIGURE_ARGS+=	--disable-nls
 .endif
 
-.if ${OPSYS} != "Linux"
-USE_GNU_ICONV=		yes		# latin1 support, iconvlist
+.if ${OPSYS} != "Darwin" && ${OPSYS} != "Linux"
+USE_GNU_ICONV=		yes	# latin1 support, iconvlist
 .endif
 
 PLIST_VARS+=		x11
diff --git a/R/PLIST b/R/PLIST
index d006b78f35..e3f56d48fd 100644
--- a/R/PLIST
+++ b/R/PLIST
@@ -1851,8 +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
-lib/R/modules/R_X11.so
-lib/R/modules/R_de.so
+${PLIST.x11}lib/R/modules/R_X11.so
+${PLIST.x11}lib/R/modules/R_de.so
 lib/R/modules/internet.so
 lib/R/modules/lapack.so
 lib/R/share/R/REMOVE.R
diff --git a/R/distinfo b/R/distinfo
index 4d024523eb..7df67dbae0 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-4.6.0.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
+BLAKE2s (R-4.6.1.tar.xz) = f2fc4cd9acdf7c4bcffdea003a1fdf83bb48c6522428d021917f4da84e764c3e
+SHA512 (R-4.6.1.tar.xz) = b62fdd0591b47999d8f8233c5ebf3b215d2db640badebcfe844082c91b44179595d2f921eb976a089aac94ea3337d2b3bdba74e4d8b5f84fd90ccf83faef2675
+Size (R-4.6.1.tar.xz) = 30960876 bytes
+SHA1 (patch-configure.ac) = d688dfd94d987b3b22d20bb040ff44ee3612f3ad
 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 dd825f6211..d6f0d217cf 100644
--- a/R/patches/patch-configure.ac
+++ b/R/patches/patch-configure.ac
@@ -1,4 +1,4 @@
-$NetBSD: patch-configure.ac,v 1.16 2026/04/14 10:33:41 jperkin Exp $
+$NetBSD: patch-configure.ac,v 1.17 2026/05/14 13:50:46 mef Exp $
 
 Do not add any system paths to R_LD_LIBRARY_PATH, it conflicts at runtime
 with what has been correctly written to the RPATH.
@@ -26,8 +26,8 @@ release    line #
  9.3       4392   withval=$with_blas; R_ARG_USE(blas)
 
 --- 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 @@
++++ configure.ac	2026-05-14 21:35:51.308108681 +0900
+@@ -33,6 +33,7 @@ m4_define([R_VERSION],
  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.
  
-@@ -328,6 +329,8 @@
+@@ -322,6 +323,8 @@ AC_ARG_ENABLE([BLAS-shlib],
  ## As from R 3.2.0 split up -L... and -lR
  if test "${want_R_shlib}" = yes; then
    LIBR0="-L\"\$(R_HOME)/lib\$(R_ARCH)\""
@@ -44,7 +44,7 @@ release    line #
    LIBR1=-lR
  else
    LIBR0=
-@@ -942,7 +945,7 @@
+@@ -936,7 +939,7 @@ case "${host_os}" in
      ## 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*)
-@@ -1874,8 +1877,8 @@
+@@ -1864,8 +1867,8 @@ dnl     ;;
      DYLIB_EXT=".dylib"
      dylib_ldflags="${darwin_dylib_ldflags}"
      MAJR_VERSION=`echo "${PACKAGE_VERSION}" | sed  -e "s/[[\.]][[1-9]]$/.0/"` 
@@ -64,7 +64,7 @@ release    line #
      ## don't use version in libRblas so we can replace it with any BLAS implementation
      RBLAS_LDFLAGS="-install_name libRblas.dylib -headerpad_max_install_names"
      ;;
-@@ -1961,7 +1964,7 @@
+@@ -1961,7 +1964,7 @@ if test -z "${CXX20}"; then
    use_CXX20=no
  fi
  if test -n "${CXX}" && test -z "${CXXSTD}"; then
@@ -73,7 +73,7 @@ release    line #
  dnl Set default C++ compiler to C++20 as available
      CXX=${CXX20}
      CXXSTD=${CXX20STD}
-@@ -2912,7 +2915,7 @@
+@@ -2895,7 +2898,7 @@ for arg in ${LDFLAGS} ${FLIBS} ${BLAS_LI
    case "${arg}" in
      -L*)
        lib=`echo ${arg} | sed "s/^-L//"`