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(math/R) updated 4.6.1 to 4.6.2
Module Name: pkgsrc-wip
Committed By: Makoto Fujiwara <makoto%if.t.u-tokyo.ac.jp@localhost>
Pushed By: mef
Date: Sun Nov 8 09:39:46 2026 +0900
Changeset: 92b14086bd066d066bfc440865a6d6f25a753205
Modified Files:
R/COMMIT_MSG
R/Makefile
R/PLIST
R/distinfo
Log Message:
(math/R) updated 4.6.1 to 4.6.2
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=92b14086bd066d066bfc440865a6d6f25a753205
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
R/COMMIT_MSG | 193 +++++++++++++++++++++++++++++++++++++++++------------------
R/Makefile | 2 +-
R/PLIST | 13 +++-
R/distinfo | 6 +-
4 files changed, 149 insertions(+), 65 deletions(-)
diffs:
diff --git a/R/COMMIT_MSG b/R/COMMIT_MSG
index 49d8411b05..e369bf8b25 100644
--- a/R/COMMIT_MSG
+++ b/R/COMMIT_MSG
@@ -1,64 +1,141 @@
-(math/R) Updated 4.6.0 to 4.6.1, build with clang still fails
+(math/R) Updated 4.6.1 to 4.6.2
-Changes in R 4.6.1:
+Changes in R 4.6.2:
- New Features:
+ Bug Fixes:
- * 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).
+ * In plain-text help (Rd2txt), paragraphs are again recognized even
+ when started with a non-indented Rd comment, fixing a regression
+ in R 4.4.0.
- * 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).
+ * rhyper(N, m, n, k) now switches to the "large" scenario when m +
+ n is larger than .Machine$integer.max, preventing integer
+ overflow, thanks to Jonathan Blood's report on R-devel.
- Bug Fixes:
+ * Fix long standing (Fortran compiler optimization related) bug in
+ nlminb with constraints, thanks to Kasper Kristensen's PR#19086
+ report and patch.
+
+ * Fix for PR#19100: seq.int was not handling non-vector along.width
+ arguments properly. Thanks to Mitchell O'Hara-Wild.
+
+ * Wrappers now duplicate even a wrapped object that might be shared
+ before returning a read-only pointer. This prevents cached
+ read-only pointers from becoming invalid. Reported by Ivan
+ Krylov.
+
+ * dummy.coef() becomes more robust to non-syntactic variable names,
+ fixing PR#18468. Thanks to Bill Dunlap and 'R Dev Day'
+ participants Vincent Arel-Bundock, Cynthia Huang, Tina Rozsos and
+ Marina Marinelli.
+
+ * Now PROTECT() in SubassignTypeFix, fixing PR#19110 thanks to
+ Kevin Ushey.
+
+ * writeChar() in a multibyte locale counts characters and bytes
+ consistently and no longer overflows, thanks to Kevin Ushey's
+ report and patch in PR#19112.
+
+ * dim(a) <- vec now checks for too large prod(vec), thanks to Kevin
+ Ushey's report and patch in PR#19109.
+
+ * Tweaks (including to the parsers) for the C23 behaviour
+ (preserving const) of strchr, strrchr and strstr. (By Brian
+ Ripley and Duncan Murdoch.)
+
+ * make check-devel now works without recommended packages.
+
+ * <matrix>[[i, j]] with negative i occasionally gives no error but
+ accesses previous content; thanks to Kevin Ushey's report and
+ very simple fix in PR#19116.
+
+ * Quartz device now correctly draws long paths (work-around for
+ Quartz built-in stroker breaking long paths). Thanks to R Dev Day
+ @ useR! 2026 contributors, notably Tomek Gieorgijewski, report in
+ PR#18680.
+
+ * strptime(ch, "...%OS<n>...") now disregards contiguous digits in
+ "<n>", for symmetry with strftime(), fulfilling Frederick Eaton's
+ wish in PR#17209, thanks to a patch by Suharto Anggono.
+
+ * strptime() now also returns NA for out of range "%OS" and a
+ correct error message in some wrong multibyte cases, fixing
+ PR#19117 comment #1 and PR#19122 by Michael Chirico;
+ additionally, some overflow to Inf times no longer result in NA.
+
+ * strptime("0", "%w") in a "C" locale now works in valid cases,
+ returning NA for invalid week numbers ("%U" or "%W"), fixing
+ PR#19124 thanks to Michael Chirico's report and notably Suharto
+ Anggono's analysis, also correctly fixing PR#15195.
+
+ * ksmooth(x,y, x.points=NULL) now returns an empty (x,y) pair
+ instead of crashing R, fixing PR#19153.
+
+ Additionally, also by Adam Berkeš, x <- rep(999,0); ksmooth(x, x,
+ x.points = 1) no longer writes out of bounds, fixing PR#19171.
+ Ditto for ksmooth(x, x, n.points = 0), PR#19219.
+
+ * besselI(1, 1e11) and besselK(..) now signal a warning and return
+ NaN instead of typically segfaulting, fixing PR#19175 thanks to
+ Ben Bolker.
+
+ Further, besselK(1, -1e11) and similar warn about too large |nu|,
+ returning NaN rather than segfaulting, fixing PR#19196 thanks to
+ Adam Berkeš.
+
+ * text.default(.., col = numeric(0)) and similar no longer segfault
+ in "instrumented" versions of R, fixing PR#19178 thanks to Jiang
+ Yuancheng's fusion-fuzz and Ivan Krylov.
+
+ * R CMD rtags (on Unix-alikes) no longer fails from a bad escape if
+ sh is bash or busybox.
+
+ * capabilities("X11") no longer incorrectly returns TRUE on a
+ Unix-alike where X11 is not actually available when built by a C
+ compiler without C23 enum base types, thanks to Trevor Davis'
+ report and patch in PR#19180.
+
+ * predict(smooth.spline(..), deriv = -99) and similar invalid deriv
+ values now signal errors instead of segfaulting, thanks to Adam
+ Berkeš' report and proposal in PR#19190.
+
+ * format(x, width = 2^31 -1) for an non-ascii character x such as x
+ = "\u00e9" now signals an error as the required width is too
+ large, rather than segfaulting, thanks to Adam Berkeš' report in
+ PR#19188.
+
+ * influence.measures() inadvertently wasn't updated along with
+ dffits(), dfbetas(), covratio(). PR#19167 by Amal Tawfik.
+
+ * If wilcox.test(..., exact=TRUE)'s p-value is close to the 0 or 1
+ boundaries, the calculation no longer suffers severely from
+ cancellation, thanks to Tasuku Kobayashi's reports and Ahmed
+ Sattar Jabbar's suggestion in PR#19144.
+
+ * Long stringed error messages are now protected from premature
+ garbage collection, fixing PR#19210, reported and analyzed by
+ Yuancheng Jiang.
+
+ * strsplit(str, perl=TRUE, bytes=TRUE) no longer accesses invalid
+ memory in case str is an invalid UTF-8 string, fixing PR#19212,
+ thanks to Kevin Ushey.
+
+ * isoreg(numeric(0)) no longer returns unallocated component yc,
+ fixing PR#19224 thanks to Kevin Ushey.
+
+ * KalmanLike(1:5, list(1,2)) and similar no longer segfault, fixing
+ PR#19217 thanks to Kevin Ushey and Adam Berkeš.
+
+ Bug Fixes (Windows):
+
+ * path.expand("~") and similar now should work correctly on Windows
+ when the user name is not in ASCII and neither %HOME% nor %USER%
+ environment variables are set, fixing PR#18949 thanks to the
+ report and patch from Ivan Krylov and Mauricio Vargas's R Dev Day
+ work.
- * '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.
+ * file.copy(*, date=TRUE) no longer opens files for exclusive
+ access when copying the file time. Consequently, the time _is_
+ copied now and concurrent attempts to open the source file should
+ work reliably, thanks to Kevin Ushey's report and patch in
+ PR#19187.
diff --git a/R/Makefile b/R/Makefile
index e5a0b16efd..4d3347eaab 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-4.6.1
+DISTNAME= R-4.6.2
CATEGORIES= math
MASTER_SITES= ${MASTER_SITE_R_CRAN:=base/R-4/}
EXTRACT_SUFX= .tar.xz
diff --git a/R/PLIST b/R/PLIST
index e3f56d48fd..eb775fa18e 100644
--- a/R/PLIST
+++ b/R/PLIST
@@ -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-saturated.svg
lib/R/library/lattice/help/figures/logo.svg
lib/R/library/lattice/help/lattice.rdb
lib/R/library/lattice/help/lattice.rdx
@@ -1085,6 +1086,7 @@ lib/R/library/spatial/CITATION
lib/R/library/spatial/DESCRIPTION
lib/R/library/spatial/INDEX
lib/R/library/spatial/Meta/Rd.rds
+lib/R/library/spatial/Meta/data.rds
lib/R/library/spatial/Meta/features.rds
lib/R/library/spatial/Meta/hsearch.rds
lib/R/library/spatial/Meta/links.rds
@@ -1096,6 +1098,9 @@ lib/R/library/spatial/PP.files
lib/R/library/spatial/R/spatial
lib/R/library/spatial/R/spatial.rdb
lib/R/library/spatial/R/spatial.rdx
+lib/R/library/spatial/data/Rdata.rdb
+lib/R/library/spatial/data/Rdata.rds
+lib/R/library/spatial/data/Rdata.rdx
lib/R/library/spatial/help/AnIndex
lib/R/library/spatial/help/aliases.rds
lib/R/library/spatial/help/paths.rds
@@ -1240,6 +1245,8 @@ lib/R/library/survival/doc/matrix.pdf
lib/R/library/survival/doc/methods.R
lib/R/library/survival/doc/methods.Rnw
lib/R/library/survival/doc/methods.pdf
+lib/R/library/survival/doc/modelframe.Rnw
+lib/R/library/survival/doc/modelframe.pdf
lib/R/library/survival/doc/multi.Rnw
lib/R/library/survival/doc/multi.pdf
lib/R/library/survival/doc/other.Rnw
@@ -1259,9 +1266,9 @@ lib/R/library/survival/doc/survival.pdf
lib/R/library/survival/doc/tiedtimes.R
lib/R/library/survival/doc/tiedtimes.Rnw
lib/R/library/survival/doc/tiedtimes.pdf
-lib/R/library/survival/doc/timedep.R
-lib/R/library/survival/doc/timedep.Rnw
-lib/R/library/survival/doc/timedep.pdf
+lib/R/library/survival/doc/timeline.R
+lib/R/library/survival/doc/timeline.Rnw
+lib/R/library/survival/doc/timeline.pdf
lib/R/library/survival/doc/validate.R
lib/R/library/survival/doc/validate.Rnw
lib/R/library/survival/doc/validate.pdf
diff --git a/R/distinfo b/R/distinfo
index 7df67dbae0..c733da6e4e 100644
--- a/R/distinfo
+++ b/R/distinfo
@@ -1,8 +1,8 @@
$NetBSD: distinfo,v 1.116 2026/04/14 10:33:41 jperkin Exp $
-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
+BLAKE2s (R-4.6.2.tar.xz) = 871a4a89ef7248dd9016ec5f62e271ea6d7d37f05e089a3dceee0557d74dfe2e
+SHA512 (R-4.6.2.tar.xz) = 1eac4cb02d23b0f7b8c72b1ffe5ad021b2754baa649a5a5dfcc1d59cb05edbeb18ad29a5c86fb9a448915ce88cc8f21abeb477cb28ef3d3dbbe0b3659db10452
+Size (R-4.6.2.tar.xz) = 29950564 bytes
SHA1 (patch-configure.ac) = d688dfd94d987b3b22d20bb040ff44ee3612f3ad
SHA1 (patch-src_extra_xdr_xdr__mem.c) = 2e607b070db8b24a6ad5501e9c7c1549bf1b1d82
SHA1 (patch-src_extra_xdr_xdr__stdio.c) = 91ea16599693e9dc14e631880fbe1c52f0f2009f
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