(math/R) revived for updating 4.4.2 to 4.4.3

[Makoto mef20 Fujiwara (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Makoto mef20 Fujiwara <makoto%if.t.u-tokyo.ac.jp@localhost>
Pushed By:	mef
Date:		Sun Mar 2 22:47:43 2025 +0900
Changeset:	a95c9afb8de2f617a1775b3434256d6eee2e3a36

Modified Files:
	R/COMMIT_MSG
	R/Makefile
	R/Makefile.extension
	R/PLIST
	R/distinfo
	R/patches/patch-m4_R.m4
Removed Files:
	R/patches/patch-configure.ac
	R/patches/patch-src_include_R__ext_Error.h

Log Message:
(math/R) revived for updating 4.4.2 to 4.4.3

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=a95c9afb8de2f617a1775b3434256d6eee2e3a36

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

diffstat:
 R/COMMIT_MSG                               | 277 +++++++----------------------
 R/Makefile                                 |  16 +-
 R/Makefile.extension                       |   4 +-
 R/PLIST                                    |  20 +--
 R/distinfo                                 |  12 +-
 R/patches/patch-configure.ac               | 133 --------------
 R/patches/patch-m4_R.m4                    |   2 +-
 R/patches/patch-src_include_R__ext_Error.h |  16 --
 8 files changed, 82 insertions(+), 398 deletions(-)

diffs:
diff --git a/R/COMMIT_MSG b/R/COMMIT_MSG
index 393528174d..887d99d9bf 100644
--- a/R/COMMIT_MSG
+++ b/R/COMMIT_MSG
@@ -1,243 +1,86 @@
-(math/R) Updated 4.3.3. to 4.4.0
+(math/R) Updated 4.4.2 to 4.4.3
 
-NEWS for R version 4.4.0 (2024-04-24)
-NEWS
+CHANGES IN R 4.4.3:
 
-R News
+  INSTALLATION:
 
-CHANGES IN R 4.4.0
-SIGNIFICANT USER-VISIBLE CHANGES:
-*   Startup banners, R --version, sessionInfo() and R CMD check no longer report
-    (64-bit) as part of the platform as this is almost universal – the increasingly rare
-    32-bit platforms will still report (32-bit).
-    On Windows, ditto for window titles.
+         * R can be installed using C23 (for example with '-std=gnu23'
+           or '-std=gnu2x') with recent compilers including 'gcc'
+           12-14, Apple 'clang' 15-16, LLVM 'clang' 17-20 and Intel
+           'icx' 2024.2.
 
-*   is.atomic(NULL) now returns FALSE, as NULL is not an atomic vector.
-    Strict back-compatibility would replace is.atomic(foo) by (is.null(foo) ||
-    is.atomic(foo)) but should happen only sparingly.
-    NEW FEATURES:
+           It can be installed with the upcoming (at the time of
+           writing) 'gcc' 15, which defaults to C23.
 
-*   The confint() methods for "glm" and "nls" objects have been copied to the
-    stats package. Previously, they were stubs which called versions in package MASS.
-    The MASS namespace is no longer loaded if you invoke (say) confint(glmfit).
-    Further, the "glm" method for profile() and the plot() and pairs() methods
-    for class "profile" have been copied from MASS to stats. (profile.nls() and
-    plot.profile.nls() were already in stats.)
+  C-LEVEL FACILITIES:
 
-*   The confint() and profile methods for "glm" objects have gained a possibility to
-    do profiling based on the Rao Score statistic in addition to the default Likelihood
-    Ratio. This is controlled by a new test = argument.
+         * The functions 'R_strtod' and 'R_atof' now allow hexadecimal
+           constants without an exponent, for compatibility with their
+           C99 versions (PR#18805).
 
-* The pairs() method for "profile" objects has been extended with a
-    which = argument to allow plotting only a subset of the
-    parameters.
+  UTILITIES:
 
-* The "glm" method for anova() computes test statistics and p-values
-  by default, using a chi-squared test or an F test depending on whether
-  the dispersion is fixed or free.  Test statistics can be suppressed by
-  giving argument test a false logical value.
+         * 'R CMD build' and 'R CMD check' now allow reference output
+           for demo scripts ('demo/<demo>.Rout.save' files) to be
+           shipped with the package, as proposed by Torsten Hothorn in
+           PR#18816.
 
-* In setRepositories() the repositories can be set using their names
-    via name = instead of index ind =.
+  BUG FIXES:
 
-* methods() and .S3methods() gain a all.names option for the (rare)
-  case where functions starting with a ‘.’ should be included.
-
-* Serializations can now be interrupted (e.g., by Ctrl-C on a
-  Unix-alike) if they take too long, e.g., from save.image(), thanks to
-  suggestions by Ivan Krylov and others on R-devel.
-
-* New startup option ‘--max-connections’ to set the maximum number of
-  simultaneous connections for the session. Defaults to 128 as before:
-  allowed values up to 4096 (but resource limits may in practice
-  restrict to smaller values).
-
-* R on Windows (since Windows 10 2004) now uses the new Segment Heap
-  allocator.  This may improve performance of some memory-intensive
-  applications.
-
-* When R packages are built, typically by R CMD build <pkg>, the new
-  --user=<build_user> option overrides the (internally determined) user
-  name, currently Sys.info()["user"] or LOGNAME. This is a (modified)
-  fulfillment of Will Landau’s suggestion in PR#17530.
-
-* tools::testInstalledBasic() gets new optional arguments outDir and
-  testSrcdir, e.g., allowing to use it in a builddir != srcdir setup,
-  and in standard “binary” Windows installation if a source ‘tests/’
-  folder is present.
-
-* range(<DT_with_Inf>, finite = TRUE) now work for objects of class
-  "Date", "POSIXct", and "POSIXlt" with infinite entries, analogously to
-  range.default(), as proposed by Davis Vaughan on R-devel. Other
-  range()-methods can make use of new function .rangeNum().
-
-* New .internalGenerics object complementing .S3PrimitiveGenerics, for
-    documentation and low-level book-keeping.
-
-* grid() now invisibly returns the x- and y- coordinates at which the
-  grid-lines were drawn.
+         * 'kappa(A, exact=TRUE)' for singular 'A' returns 'Inf' more
+           generally, fixing PR#18817 reported by Mikael Jagan.
 
-*   norm(., type) now also works for complex matrices.
+         * Fixed URLs of the sun spots ('sunspot.month' etc) data sets
+           and mention future changes due to recalibration.
 
-* kappa(., exact = TRUE, norm = *) now works for all norms and also
-  for complex matrices. In symmetric / triangular cases, the new
-  argument uplo = "U" | "L" allows the upper or lower triangular part to
-  be specified.
+         * The parser now accepts hexadecimal constants with a decimal
+           point without an exponent (taken as 'p0') as documented in
+           '?NumericConstants' (PR#18819).
 
-* memDecompress(type = "unknown") recognizes compression in the
-    default ‘zlib’ format as used by memCompress(type = "gzip").
+         * 'rbind()' now works correctly when inputs include a raw
+           vector and a logical, integer or double vector - previously
+           the inclusion of the latter was garbled.
 
-* memCompress() and memDecompress() will use the libdeflate library
-  (https: //github.com/ebiggers/libdeflate) if installed. This uses the
-  same type of compression for type = "gzip" but is 1.5-2x faster than
-  the system libz library on some common platforms: the speed-up may
-  depend on the library version.
+         * 'smooth.spline()' checks validity of its arguments
+           'df.offset' and 'penalty': it could segfault if they were
+           'NULL'.
 
-* diff() for objects of class "Date", "POSIXct", and "POSIXlt" accepts
-    a units argument passed via ....
+         * 'isGeneric(<primitive>, fdef=*, getName=TRUE)' now also
+           returns the name instead of just 'TRUE', fixing PR#18829
+           reported by Mikael Jagan.
 
-* Dynamic help now does a much better job of rendering package
-    ‘DESCRIPTION’ metadata.
+         * 'isGeneric(fdef = print)' now works, fixing PR#18369 thanks
+           to Mikael Jagan.
 
-* Rprof() gains an event argument and support for elapsed (real) time
-profiling on Unix (PR#18076).
+         * 'sort(x, method = "qsort")' made illegal accesses when 'x'
+           has length 0.
 
-*   filled.contour() gains a key.border argument.
+         * 'dir.create()' is protected against being passed an empty
+           string as its 'path' argument.
 
-* tools::update_pkg_po() gets arguments pot_make and mo_make for not
-  re-making the corresponding files, and additionally a verbose
-  argument.
+         * Silent integer overflow could occur in the 'exact'
+           computations for 'fisher.test()' for unrealistic inputs:
+           this is now an error.
 
-* Hexadecimal string colour specifications are now accepted in short
-  form, so, for example, we can use "#123", which is equivalent to
-  "#112233".  Thanks to MikeFC for the original idea and Ella Kaye,
-  Malcolm Barrett, George Stagg, and Hanne Oberman for the patch.
+         * Some invalid C-level memory accesses are avoided for
+           'loglin(, margin = NULL)'.
 
-*   Plain-text help shows \var markup by angle brackets.
+           'loglin(, param = TRUE)' no longer gives an error in corner
+           cases such as a one-dimensional input.
 
-* The new experimental primitive function declare() is intended to
-  eventually allow information about R code to be communicated to the
-  interpreter, compiler, and code analysis tools. The syntax for
-  declarations is still being developed.
+         * 'dev.capabilities() $ events' now reports '"Idle"' if the
+           device provides it, fixing PR#18836, thanks to Trevor Davis.
 
-* Functions psmirnov(), qsmirnov() and rsmirnov() in package stats
-  have had argument two.sided renamed to alternative, to take into
-  account that the permutation distributions of the one-sided statistics
-  can be different in the case of ties. Consequence of PR#18582.
+         * 'arima(.., seasonal = <wrong-vector>)' correctly errors now,
+           ditto for 'arima0()', thanks to Norbert Kuder's report on
+           the R-devel list.
 
-*   sort() is now an implicit S4 generic in methods.
+         * 'binomial(<link>)$linkinv(eta)' and '.. $mu.eta(eta)' now
+           also work for '"logit"' link when 'is.integer(eta)'.
 
-* Formatting and printing, format(z), print(z), of complex vectors z
-  no longer zap relatively small real or imaginary parts to zero, fixing
-  PR#16752. This is an API change, as it was documented previously to
-  round real and imaginary parts together on purpose, producing nicer
-  looking output. As mentioned, e.g. in the PR, this change is
-  compatible with many other “R-like” programming environments.  We have
-  simplified the internal code and now basically format the real and
-  imaginary parts independently of each other.
+         * 'as.roman(x)' now should work platform independently, also
+           for, e.g., 'x = "IIIII"' (= V) and 'x = "IIIIII"' (= VI).
 
-* New experimental functions Tailcall() and Exec() to support writing
-    stack-spaceefficient recursive functions.
-
-* Where characters are attempted to be plotted by pdf(), postscript()
-  and xfig() which are not in the selected 8-bit character set (most
-  often Latin-1) and the R session is using a UTF-8 locale, the warning
-  messages will show the UTF-8 character rather than its bytes and one
-  dot will be substituted per character rather than per byte.
-  (Platforms whose iconv() does transliteration silently plot the
-  transliteration.)  In a UTF-8 locale some transliterations are now
-  done with a warning (e.g., dashes and Unicode minus to hyphen,
-  ligatures are expanded, permille (‘‰’) is replaced by ‘o/oo’),
-  although the OS may have got there first. These are warnings as they
-  will continue to be replaced by dots in earlier versions of R.
-
-* The matrix multiplication functions crossprod() and tcrossprod() are
-  now also primitive and S3 generic, as %*% had become in R 4.3.0.
-
-* source() and example() have a new optional argument catch.aborts
-  which allows continued evaluation of the R code after an error.
-
-* The non-Quartz tiff() devices allow additional types of compression
-  if supported by the platform’s ‘libtiff’ library.
-
-*   The list of base and recommended package names is now provided by
-    tools::standard_package_names().
-
-* cairo_pdf() and cairo_ps() default to onefile = TRUE to closer match
-  pdf() and postscript().
-
-* New option catch.script.errors provides a documented way to catch
-  errors and then continue in non-interactive use.
-
-* L %||% R newly in base is an expressive idiom for the phrases
-  if(!is.null(L)) L else R or if(is.null(L)) R else L.
-
-* The return value from warnings() now always inherits from "warnings"
-    as documented, now also in the case of no warnings where it
-    previously returned NULL.
-
-*   as.complex("1i") now returns 0 + 1i instead of NA with a warning.
-
-* z <- c(NA, 1i) now keeps the imaginary part Im(z[1]) == 0, no longer
-  coercing to NA_complex_. Similarly, cumsum(z) correctly sums real and
-  imaginary parts separately, i.e., without “crosstalk” in case of NAs.
-
-*   On Alpine Linux iconv() now maps "latin2", "latin-2", "latin9" and "latin-9"
-    to encoding names the OS knows about (case-insensitively).
-
-* iconv(sub = "Unicode") now always zero-pads to four (hex) digits,
-  rather than to 4 or 8. (This seems to have become the convention
-  once Unicode restricted the number of Unicode points to 221 − 1
-  and so will never need more than 6 digits.)
-
-*   NCOL(NULL) now returns 0 instead of 1, for consistency with cbind().
-
-* The information for the Euro glyph missing from the Adobe ‘.afm’
-  files for the Courier, Helvetica and Times families has been copied
-  from their URW equivalents – this will improve vertical centring in
-  the pdf() and postscript() devices.
-
-* The included BLAS sources have been updated to those shipped with
-  LAPACK version 3.12.0. The changes are almost entirely cosmetic.
-
-
-*   The included LAPACK sources have been updated to version 3.12.0 and some further
-double-complex routines added.
-
-* There are new font families for the 2014–5 URW 2.0 fonts (see ?pdf)
-  which are included in recent versions of Ghostscript. These have font
-  widths for most Greek glyphs and a few others which were missing from
-  the original versions (whose font families remain available for
-  reproducibility, although Ghostscript-based viewers will render using
-  the 2.0 versions).
-
-* Improve the large-n efficiency of as.matrix(<dist>), thanks an R
-  contributors effort, notably by Tim Taylor and Heather Turner, see
-  PR#18660.
-
-*   The default and numeric methods of all.equal() get a check.class option.
-
-* zapsmall() gets new optional arguments, function mFUN and min.d, for
-  extra flexibility; fulfills a wish in PR#18199. Also, it is now an
-  implicit S4 generic in package methods.
-
-*   The Rd filter for aspell() gains an ignore argument.
-
-* New generic function sort_by(), primarily useful for the data.frame
-  method which can be used to sort rows of a data frame by one or more
-  columns.
-
-*   The icence headers for the RPC code in ‘src/extra/xdr’ have been updated to use
-    the GPL-compatible licence published by Oracle America in 2010.
-
-*   New function pkg2HTML() in tools to create single-page HTML reference manuals for
-    R packages.
-
-* The byte code evaluator now uses less C stack space for recursive
-  calls to bytecompiled functions. It also makes more of an effort to
-  avoid allocations for scalar return values.
-
-* New completion option backtick (disabled by default) allows
-  non-syntactic completions to be wrapped in backquotes. This is
-  currently only useful for Jupyter notebooks via the IRkernel package,
-  and may cause problems for other backends.
+         * 'R CMD Rd2pdf' works again on an installed package directory
+           containing LaTeX help (from option '--latex'), thanks to a
+           report by Peter Ruckdeschel.
diff --git a/R/Makefile b/R/Makefile
index b11c2bb337..9f85419f3a 100644
--- a/R/Makefile
+++ b/R/Makefile
@@ -1,10 +1,10 @@
-# $NetBSD: Makefile,v 1.251 2024/02/15 07:48:50 markd Exp $
+# $NetBSD: Makefile,v 1.266 2025/03/02 10:26:38 mef Exp $
 
 #
 # If updating this package, please try to ensure PLIST.Darwin is kept in sync
 # to avoid unnecessarily breaking macOS users.
 #
-DISTNAME=	R-4.4.0
+DISTNAME=	R-4.4.3
 CATEGORIES=	math
 MASTER_SITES=	${MASTER_SITE_R_CRAN:=base/R-4/}
 
@@ -35,6 +35,8 @@ CONFIGURE_ARGS+=	--with-tcltk
 CONFIGURE_ARGS+=	--with-tcl-config=${BUILDLINK_PREFIX.tcl}/lib/tclConfig.sh
 CONFIGURE_ARGS+=	--with-tk-config=${BUILDLINK_PREFIX.tk}/lib/tkConfig.sh
 
+LDFLAGS+=		${COMPILER_RPATH_FLAG}${PREFIX}/lib/R/lib
+
 .include "../../mk/bsd.prefs.mk"
 .if ${OPSYS} == "NetBSD" || ${OPSYS} == "FreeBSD"
 CONFIGURE_ARGS+=	--enable-long-double=no
@@ -149,18 +151,11 @@ INSTALL_SCRIPT=		${INSTALL} ${COPY} -m ${BINMODE}
 #TOOL_DEPENDS+=		tex-mptopdf-[0-9]*:../../graphics/tex-mptopdf
 #TOOL_DEPENDS+=		tex-pdftex-def-[0-9]*:../../print/tex-pdftex
 
-#SUBST_CLASSES+=		rpath
-#SUBST_STAGE.rpath=	pre-configure
-#SUBST_FILES.rpath=	configure.ac
-#SUBST_VARS.rpath=	COMPILER_RPATH_FLAG
-
 SUBST_CLASSES+=		fixwrap
 SUBST_STAGE.fixwrap=	post-build
 SUBST_FILES.fixwrap=	libtool
 SUBST_SED.fixwrap=	-e "s,${WRAPPER_BINDIR}/libtool,${PKG_LIBTOOL},g"
 
-BUILDLINK_API_DEPENDS.bzip2+=	bzip2>=1.0.5
-
 # failed to convert strong functions and variables: Invalid type identifier
 CTF_FILES_SKIP+=	lib/R/library/mgcv/libs/mgcv.so
 
@@ -184,8 +179,9 @@ fix-darwin-install-name:
 
 # remove orig version left out
 post-install:
-	${RM}	${DESTDIR}${PREFIX}/lib/R/library/survival/NEWS.Rd.orig
+	${RM}	-f ${DESTDIR}${PREFIX}/lib/R/library/survival/NEWS.Rd.orig
 
+BUILDLINK_API_DEPENDS.bzip2+=	bzip2>=1.0.5
 .include "../../archivers/bzip2/buildlink3.mk"
 .include "../../archivers/xz/buildlink3.mk"
 .include "../../converters/libiconv/buildlink3.mk"
diff --git a/R/Makefile.extension b/R/Makefile.extension
index 332bca4bab..67540d90de 100644
--- a/R/Makefile.extension
+++ b/R/Makefile.extension
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile.extension,v 1.28 2022/03/23 21:16:44 wiz Exp $
+# $NetBSD: Makefile.extension,v 1.29 2024/11/22 15:28:52 jperkin Exp $
 #
 # This Makefile fragment is included by packages for R library packages.
 #
@@ -24,7 +24,7 @@ R_PKGVER?=	${DISTNAME:C/.*_//}
 .else
 DISTNAME?=	${R_PKGNAME}_${R_PKGVER}
 .endif
-PKGNAME?=	R-${R_PKGNAME}-${R_PKGVER:S/-/./}
+PKGNAME?=	R-${R_PKGNAME}-${R_PKGVER:S/-/./g}
 MASTER_SITES?=	${MASTER_SITE_R_CRAN:=contrib/} \
 		${MASTER_SITE_R_CRAN:=contrib/Archive/${R_PKGNAME}/}
 DIST_SUBDIR?=	R
diff --git a/R/PLIST b/R/PLIST
index 53f34c649c..7dba22ad74 100644
--- a/R/PLIST
+++ b/R/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD$
+@comment $NetBSD: PLIST,v 1.42 2024/11/01 07:12:59 mef Exp $
 bin/R
 bin/Rscript
 info/R-FAQ.info.gz
@@ -385,20 +385,13 @@ lib/R/library/Matrix/po/lt/LC_MESSAGES/Matrix.mo
 lib/R/library/Matrix/po/lt/LC_MESSAGES/R-Matrix.mo
 lib/R/library/Matrix/po/pl/LC_MESSAGES/Matrix.mo
 lib/R/library/Matrix/po/pl/LC_MESSAGES/R-Matrix.mo
-lib/R/library/Matrix/scripts/AMD.patch
-lib/R/library/Matrix/scripts/CAMD.patch
-lib/R/library/Matrix/scripts/CCOLAMD.patch
-lib/R/library/Matrix/scripts/CHOLMOD.patch
-lib/R/library/Matrix/scripts/COLAMD.patch
-lib/R/library/Matrix/scripts/CXSparse.patch
-lib/R/library/Matrix/scripts/SuiteSparse_config.patch
-lib/R/library/Matrix/scripts/api.patch
+lib/R/library/Matrix/scripts/SuiteSparse.patch
+lib/R/library/Matrix/scripts/cholmod.h.patch
 lib/R/library/Matrix/scripts/disclaimer.txt
 lib/R/library/Matrix/scripts/rules.mk
 lib/R/library/Matrix/scripts/rules.sh
 lib/R/library/Matrix/scripts/sources.mk
 lib/R/library/Matrix/scripts/ssget.sh
-lib/R/library/Matrix/scripts/wall.patch
 lib/R/library/Matrix/test-tools-1.R
 lib/R/library/Matrix/test-tools-Matrix.R
 lib/R/library/Matrix/test-tools.R
@@ -775,6 +768,7 @@ lib/R/library/grDevices/html/00Index.html
 lib/R/library/grDevices/html/R.css
 lib/R/library/grDevices/icc/srgb
 lib/R/library/grDevices/icc/srgb.flate
+lib/R/library/grDevices/libs/cairo.so
 lib/R/library/grDevices/libs/grDevices.so
 lib/R/library/graphics/DESCRIPTION
 lib/R/library/graphics/INDEX
@@ -1234,13 +1228,13 @@ lib/R/library/survival/doc/compete.pdf
 lib/R/library/survival/doc/concordance.R
 lib/R/library/survival/doc/concordance.Rnw
 lib/R/library/survival/doc/concordance.pdf
-lib/R/library/survival/doc/discrim.R
-lib/R/library/survival/doc/discrim.Rnw
-lib/R/library/survival/doc/discrim.pdf
 lib/R/library/survival/doc/index.html
 lib/R/library/survival/doc/matrix.R
 lib/R/library/survival/doc/matrix.Rnw
 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/multi.Rnw
 lib/R/library/survival/doc/multi.pdf
 lib/R/library/survival/doc/other.Rnw
diff --git a/R/distinfo b/R/distinfo
index 4f0164c270..8c4fa35186 100644
--- a/R/distinfo
+++ b/R/distinfo
@@ -1,10 +1,10 @@
-$NetBSD: distinfo,v 1.103 2024/02/15 07:48:50 markd Exp $
+$NetBSD: distinfo,v 1.111 2025/03/02 10:26:38 mef Exp $
 
-BLAKE2s (R-4.4.0.tar.gz) = 31efebb6f183d6e754b82dfb14b4715659a01d5ee95b86048d6127f884d42d6a
-SHA512 (R-4.4.0.tar.gz) = 8f44eac49c58db7f161732135be4d1757f65b18545f3f15c463d499794735d02f4a4cb9bacff90d16e80b624ead8aa0af16899cf7654b6cb91a46868e405bd17
-Size (R-4.4.0.tar.gz) = 37335563 bytes
-SHA1 (patch-configure.ac) = 91bed37afc2ee2f68695f8496c56ae23aaf42b43
+BLAKE2s (R-4.4.3.tar.gz) = c7860018ef691608dfa505c2bbeb7e015d03d106e8590587b49d1eac63449cda
+SHA512 (R-4.4.3.tar.gz) = 2a1d1e5ee2e18c928e2b3e58df372083b4bbd0822863a8441404999209035436e236c8ffe3970827fbf3d765157365800ebb0bb46f361c6abe473ddec30be06f
+Size (R-4.4.3.tar.gz) = 40234425 bytes
 SHA1 (patch-m4_R.m4) = 3e1d390d8aa9895aee7cb479ddab371d82562b88
-SHA1 (patch-src_include_R__ext_Error.h) = bc55a8bba6bf931e3f6794577e63bfafdfc740cf
+SHA1 (patch-src_extra_xdr_xdr__mem.c) = 2e607b070db8b24a6ad5501e9c7c1549bf1b1d82
+SHA1 (patch-src_extra_xdr_xdr__stdio.c) = e4d8ace08ad282f44113941dd6a3b194769b8167
 SHA1 (patch-src_library_stats_src_Makefile.in) = 4eb93292858392792c37a706399e2cef91821bbe
 SHA1 (patch-src_main_character.c) = c1be2cae404ecbdd547343b70e9d072e9e1d5549
diff --git a/R/patches/patch-configure.ac b/R/patches/patch-configure.ac
deleted file mode 100644
index 0c017d530e..0000000000
--- a/R/patches/patch-configure.ac
+++ /dev/null
@@ -1,133 +0,0 @@
-$NetBSD: patch-configure.ac,v 1.8 2024/01/08 23:13:03 mef Exp $
-
-Do not include system paths in R_LD_LIBRARY_PATH.
-NetBSD, FreeBSD, DragonFly, Darwin and Solaris fixes
-
---- configure.ac.orig	2024-03-27 08:02:03.000000000 +0900
-+++ configure.ac	2024-04-29 00:00:51.788804133 +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])
-+AC_CONFIG_MACRO_DIR([m4])
- 
- ### * Information on the package.
- 
-@@ -136,7 +137,7 @@ R_CONFIG_ARGS="${ac_configure_args}"
- AC_SUBST(R_CONFIG_ARGS)
- 
- ## Shortcut for musl which refuses to identify itself at C level
--if test "${host_os}" == "linux-musl"; then
-+if test "${host_os}" = "linux-musl"; then
-   AC_DEFINE(OS_MUSL, 1, [Define if running on Linux-musl])
- fi
- 
-@@ -316,7 +317,7 @@ AC_ARG_ENABLE([BLAS-shlib],
- 
- ## As from R 3.2.0 split up -L... and -lR
- if test "${want_R_shlib}" = yes; then
--  LIBR0="-L\"\$(R_HOME)/lib\$(R_ARCH)\""
-+  LIBR0="-Wl,-R${prefix}/lib/R/lib\$(R_ARCH) -L\"\$(R_HOME)/lib\$(R_ARCH)\""
-   LIBR1=-lR
- else
-   LIBR0=
-@@ -898,7 +899,7 @@ case "${host_os}" in
-     ## Not so bad in later versions of Darwin, 
-     ## where DYLD_FALLBACK_LIBRARY_PATH is used (see below).
-     ;;
--  *)
-+  donotuse*)
-     for arg in ${LDFLAGS}; do
-       case "${arg}" in
-         -L*)
-@@ -1549,7 +1550,7 @@ rm -f libconftest${DYLIB_EXT} conftest.c
-     fpicflags="${darwin_pic}"
-     shlib_cxxldflags="${shlib_ldflags}"
-     ;;
--  freebsd*)
-+  freebsd*|dragonfly*)
-     ## maybe this needs to depend on the compiler:
-     ## -export-dynamic used to work, but does not with clang.
-     ## Seems FreeBSD has used the GNU linker since at least 3.0 (Oct 1998)
-@@ -1638,6 +1639,12 @@ dnl     ;;
-     ;;
-   netbsd*)
-     ## See the comments about FreeBSD
-+    fpicflags="-fPIC"
-+    case "${host_cpu}" in
-+      powerpc*)
-+      cpicflags="-fPIC"
-+      ;;
-+    esac
-     if ${CPP} - -dM < /dev/null | grep __ELF__ >/dev/null ; then
-       main_ldflags="-Wl,--export-dynamic"
-       shlib_ldflags="-shared"
-@@ -1674,22 +1681,22 @@ dnl     ;;
-   solaris*)
- ## SPARC has only an 8k global object table, 1024 entries on 64-bit,
- ## so need PIC not pic.  They are the same on other Solaris platforms.
--    shlib_ldflags="-G"
--    shlib_cxxldflags="-G"
-    if test "${GCC}" = yes; then
-+      shlib_ldflags="-shared"
-+      shlib_cxxldflags="-shared"
-       cpicflags="-fPIC"
-       ld=`${CC} -print-prog-name=ld`
-       ldoutput=`${ld} -v 2>&1 | grep GNU`
-       if test -n "${ldoutput}"; then
- 	main_ldflags="-Wl,-export-dynamic"
--	shlib_ldflags="-shared"
--        shlib_cxxldflags="-shared"
-       else
-         ## it seems gcc c 4.6.2 needs this with Solaris linker
- 	shlib_ldflags="-shared"
-         shlib_cxxldflags="-shared"
-       fi
-     else
-+      shlib_ldflags="-G"
-+      shlib_cxxldflags="-G"
-       cpicflags="-KPIC"
-       if test "`basename ${CXX}`" = "CC" ; then
-         ## Forte version 7 needs -lCstd: Forte 6 does not.	
-@@ -1768,7 +1775,7 @@ fi
- : ${CXXPICFLAGS="${cxxpicflags}"}
- if test -n "${CXX}" -a -z "${CXXPICFLAGS}"; then
-   case "${host_os}" in
--    aix*|mingw*|msys)
-+    aix*|mingw*|msys|darwin*)
-       ;;
-     *)
-       warn_cxxpicflags="I could not determine CXXPICFLAGS."
-@@ -1828,8 +1835,10 @@ dnl     ;;
-     MAJR_VERSION=`echo "${PACKAGE_VERSION}" | sed  -e "s/[[\.]][[1-9]]$/.0/"` 
-     LIBR_LDFLAGS="-install_name libR.dylib -compatibility_version ${MAJR_VERSION}  -current_version ${PACKAGE_VERSION}  -headerpad_max_install_names"
-     RLAPACK_LDFLAGS="-install_name libRlapack.dylib -compatibility_version ${MAJR_VERSION} -current_version ${PACKAGE_VERSION}  -headerpad_max_install_names"
-+    LIBR_LDFLAGS="-install_name ${PREFIX}/lib/R/lib/libR.dylib -compatibility_version ${MAJR_VERSION}  -current_version ${PACKAGE_VERSION}  -headerpad_max_install_names"
-+    RLAPACK_LDFLAGS="-install_name ${PREFIX}/lib/R/lib/libRlapack.dylib -compatibility_version ${MAJR_VERSION} -current_version ${PACKAGE_VERSION}  -headerpad_max_install_names"
-     ## 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"
-+    RBLAS_LDFLAGS="-install_name ${PREFIX}/lib/R/lib/libRblas.dylib -headerpad_max_install_names"
-     ;;
- dnl   hpux*)
- dnl     ## Needs to avoid embedding a relative path ../../../bin.
-@@ -2825,7 +2834,7 @@ case "${host_os}" in
-     r_ld_library_defaults="/usr/lib64:/lib64:/usr/lib:/lib"
-     ;;
-   solaris*)
--    r_ld_library_defaults="/usr/lib:/lib"
-+    r_ld_library_defaults="/usr/lib:/lib:/usr/lib/amd64:/lib/amd64:/usr/lib/64:/lib/64"
-     ;;
-   *)
-     r_ld_library_defaults=
-@@ -2995,9 +3004,9 @@ sdk_OK=no)
- dnl No longer used as we only build (or not) BLAS and LAPACK shims
- dnl  AC_DEFINE(USE_NEW_ACCELERATE, 1, [Define to use Apple's (new) Accelerate])
- fi
--AM_CONDITIONAL(BUILD_NEW_ACCELERATE, [test "x${use_accelerate}" == xyes])
-+AM_CONDITIONAL(BUILD_NEW_ACCELERATE, [test "x${use_accelerate}" = xyes])
- AM_CONDITIONAL(BUILD_NEW_ACCELERATE_LAPACK,
--              [test "x${use_accelerate_lapack}" == xyes])
-+              [test "x${use_accelerate_lapack}" = xyes])
- 
- dnl record compiler versions
- CC_VER=`${CC} --version | ${SED} -n 1p`
diff --git a/R/patches/patch-m4_R.m4 b/R/patches/patch-m4_R.m4
index 2daf7f1126..3032484c7a 100644
--- a/R/patches/patch-m4_R.m4
+++ b/R/patches/patch-m4_R.m4
@@ -1,4 +1,4 @@
-$NetBSD: patch-m4_R.m4,v 1.5 2024/01/08 23:15:39 mef Exp $
+$NetBSD: patch-m4_R.m4,v 1.6 2024/05/27 20:45:14 mef Exp $
 
 Ensure tests for clog & co. fail, not just emit warning
 
diff --git a/R/patches/patch-src_include_R__ext_Error.h b/R/patches/patch-src_include_R__ext_Error.h
deleted file mode 100644
index 490c32f358..0000000000
--- a/R/patches/patch-src_include_R__ext_Error.h
+++ /dev/null
@@ -1,16 +0,0 @@
-$NetBSD: patch-src_include_R__ext_Error.h,v 1.1 2024/03/05 16:12:33 jperkin Exp $
-
-Fix building with C++.
-
---- src/include/R_ext/Error.h.orig	2024-03-05 16:09:06.557665563 +0000
-+++ src/include/R_ext/Error.h
-@@ -35,7 +35,8 @@ extern "C" {
-  * In C11 there is _Noreturn * (or noreturn in header <stdnoreturn.h>).
-  */
- #if defined NORET
--#elif (defined(__STDC_VERSION__) && __STDC_VERSION__ >= 202301L)
-+#elif (defined(__STDC_VERSION__) && __STDC_VERSION__ >= 202301L) || \
-+      (defined(__cplusplus) && __cplusplus >= 201103L)
- # define NORET [[noreturn]]
- #elif defined(__STDC_VERSION__) && __STDC_VERSION__ >= 201102L
- # define NORET _Noreturn