CVS commit: pkgsrc/math/R

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Sat Jun 27 10:59:23 UTC 2026

Modified Files:
        pkgsrc/math/R: Makefile PLIST distinfo

Log Message:
(math/R) Updated 4.6.0 to 4.6.1, build with clang (21.1.18) may be OK for now.

Changes in R 4.6.1:

  New Features:

         * 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).

         * 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).

  Bug Fixes:

         * 'abbreviate(<non-ASCII>)' now works better, using
           'iswlower()' and '*upper()' to treat "wide" characters,
           thanks to Kevin's PR#19058.

         * 'cut(1:11, {})' now signals an error for the invalid
           'breaks', fixing PR#19057, thanks to Kevin Ushey.

         * '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.

         * '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.

           Further, 'stl()' is now based on C code, translated from
           previous Fortran, triggered by a flang 22 compiler
           optimization bug ('-O2').

         * 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.

         * '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.

         * 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).

         * 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.

         * '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.

         * In 'methods', 'as()' now correctly coerces S4 objects to S4
           superclasses extending old-style classes, instead of
           returning only the S3 part.


To generate a diff of this commit:
cvs rdiff -u -r1.286 -r1.287 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.48 -r1.49 pkgsrc/math/R/PLIST
cvs rdiff -u -r1.118 -r1.119 pkgsrc/math/R/distinfo

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:1.286 pkgsrc/math/R/Makefile:1.287
--- pkgsrc/math/R/Makefile:1.286        Thu May 21 13:28:34 2026
+++ pkgsrc/math/R/Makefile      Sat Jun 27 10:59:23 2026
@@ -1,11 +1,10 @@
-# $NetBSD: Makefile,v 1.286 2026/05/21 13:28:34 adam Exp $
+# $NetBSD: Makefile,v 1.287 2026/06/27 10:59:23 mef Exp $
 
 #
 # 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
-PKGREVISION=   1
+DISTNAME=      R-4.6.1
 CATEGORIES=    math
 MASTER_SITES=  ${MASTER_SITE_R_CRAN:=base/R-4/}
 EXTRACT_SUFX=  .tar.xz

Index: pkgsrc/math/R/PLIST
diff -u pkgsrc/math/R/PLIST:1.48 pkgsrc/math/R/PLIST:1.49
--- pkgsrc/math/R/PLIST:1.48    Mon May 18 13:35:43 2026
+++ pkgsrc/math/R/PLIST Sat Jun 27 10:59:23 2026
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.48 2026/05/18 13:35:43 adam Exp $
+@comment $NetBSD: PLIST,v 1.49 2026/06/27 10:59:23 mef Exp $
 bin/R
 bin/Rscript
 info/R-FAQ.info.gz

Index: pkgsrc/math/R/distinfo
diff -u pkgsrc/math/R/distinfo:1.118 pkgsrc/math/R/distinfo:1.119
--- pkgsrc/math/R/distinfo:1.118        Thu May 14 13:50:46 2026
+++ pkgsrc/math/R/distinfo      Sat Jun 27 10:59:23 2026
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.118 2026/05/14 13:50:46 mef Exp $
+$NetBSD: distinfo,v 1.119 2026/06/27 10:59:23 mef 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
+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