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(math/R) update to 4.5.3
Module Name: pkgsrc-wip
Committed By: Makoto Fujiwara <makoto%if.t.u-tokyo.ac.jp@localhost>
Pushed By: mef
Date: Sat Apr 25 09:18:28 2026 +0900
Changeset: 2fa7a24d2995bdd386747176e677e1f183ccde2e
Modified Files:
R/Makefile
R/PLIST
R/PLIST.Darwin
R/distinfo
R/patches/patch-configure.ac
R/patches/patch-src_extra_xdr_xdr__stdio.c
R/patches/patch-src_include_R__ext_Error.h
R/patches/patch-src_library_grDevices_src_devPS.c
Log Message:
(math/R) update to 4.5.3
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=2fa7a24d2995bdd386747176e677e1f183ccde2e
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
R/Makefile | 10 ++++--
R/PLIST | 3 +-
R/PLIST.Darwin | 3 +-
R/distinfo | 10 +++---
R/patches/patch-configure.ac | 44 ++++++++++++++++++++---
R/patches/patch-src_extra_xdr_xdr__stdio.c | 2 +-
R/patches/patch-src_include_R__ext_Error.h | 2 +-
R/patches/patch-src_library_grDevices_src_devPS.c | 2 +-
8 files changed, 59 insertions(+), 17 deletions(-)
diffs:
diff --git a/R/Makefile b/R/Makefile
index 5064867d3f..fb4768e281 100644
--- a/R/Makefile
+++ b/R/Makefile
@@ -1,10 +1,10 @@
-# $NetBSD: Makefile,v 1.266 2025/03/02 10:26:38 mef Exp $
+# $NetBSD: Makefile,v 1.282 2026/04/14 10:33:41 jperkin Exp $
#
# If updating this package, please try to ensure PLIST.Darwin is kept in sync
# to avoid unnecessarily breaking macOS users.
#
-DISTNAME= R-4.5.2
+DISTNAME= R-4.5.3
CATEGORIES= math
MASTER_SITES= ${MASTER_SITE_R_CRAN:=base/R-4/}
@@ -19,6 +19,10 @@ USE_GCC_RUNTIME= yes
# above line mentions c23 as default compiler for R, but c23 (gcc15) is N/A ?
# USE_CC_FEATURES+= c23
+# R-4.5.2/tests/Pkgs/pkgA: Cannot restore extended attributes: com.apple.provenance com.apple.provenance: Unknown error: -1
+USE_TOOLS+= gtar
+EXTRACT_USING= gtar
+
BUILD_TARGET= all info
INSTALL_TARGET= install install-info
TEST_TARGET= check
@@ -154,6 +158,8 @@ INSTALL_SCRIPT= ${INSTALL} ${COPY} -m ${BINMODE}
#TOOL_DEPENDS+= tex-latexconfig-[0-9]*:../../print/tex-latexconfig
#TOOL_DEPENDS+= tex-mptopdf-[0-9]*:../../graphics/tex-mptopdf
#TOOL_DEPENDS+= tex-pdftex-def-[0-9]*:../../print/tex-pdftex
+TOOL_DEPENDS+= p5-Text-Unidecode-[0-9]*:../../textproc/p5-Text-Unidecode
+TOOL_DEPENDS+= p5-Locale-libintl-[0-9]*:../../misc/p5-Locale-libintl
SUBST_CLASSES+= fixwrap
SUBST_STAGE.fixwrap= post-build
diff --git a/R/PLIST b/R/PLIST
index 72408630fd..61da1dcde7 100644
--- a/R/PLIST
+++ b/R/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD$
+@comment $NetBSD: PLIST,v 1.45 2026/03/12 11:22:57 mef Exp $
bin/R
bin/Rscript
info/R-FAQ.info.gz
@@ -229,6 +229,7 @@ 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
diff --git a/R/PLIST.Darwin b/R/PLIST.Darwin
index 8cde1da877..97d8f1ef17 100644
--- a/R/PLIST.Darwin
+++ b/R/PLIST.Darwin
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST.Darwin,v 1.14 2023/12/24 15:17:38 wiz Exp $
+@comment $NetBSD: PLIST.Darwin,v 1.15 2026/03/12 11:22:57 mef Exp $
@comment
@comment The configure script has explicit check for darwin and sets
@comment --with-internal-tzcode=yes
@@ -111,6 +111,7 @@ lib/R/share/zoneinfo/America/Ciudad_Juarez
lib/R/share/zoneinfo/America/Coral_Harbour
lib/R/share/zoneinfo/America/Cordoba
lib/R/share/zoneinfo/America/Costa_Rica
+lib/R/share/zoneinfo/America/Coyhaique
lib/R/share/zoneinfo/America/Creston
lib/R/share/zoneinfo/America/Cuiaba
lib/R/share/zoneinfo/America/Curacao
diff --git a/R/distinfo b/R/distinfo
index 5a0a28b3c4..4d2438016e 100644
--- a/R/distinfo
+++ b/R/distinfo
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.111 2025/03/02 10:26:38 mef Exp $
+$NetBSD: distinfo,v 1.116 2026/04/14 10:33:41 jperkin Exp $
-BLAKE2s (R-4.5.2.tar.gz) = 89aaf25d047df226ec7340bf5550db5223163bec0b5ff1d5a3bfae691aa2106a
-SHA512 (R-4.5.2.tar.gz) = abc4ff1a1b18a1f480e7bceb3267074e30453b5a571034b4c2a1c53e1650a1bafaf86bc6ca37f117a2e4f6617039dedeedef4ba8743f38720fc70e4bed2ff0a4
-Size (R-4.5.2.tar.gz) = 40546249 bytes
-SHA1 (patch-configure.ac) = 61904b7918019204634d61bce2421c01c81ed640
+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
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 2de1d5348c..05916ccb2d 100644
--- a/R/patches/patch-configure.ac
+++ b/R/patches/patch-configure.ac
@@ -1,4 +1,9 @@
-$NetBSD$
+$NetBSD: patch-configure.ac,v 1.16 2026/04/14 10:33:41 jperkin 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.
+
+Fix Darwin -install_name path for libR.dylib
on NetBSD/amd64 9.4: getting
@@ -20,9 +25,9 @@ release line #
10.99.12 4770 withval=$with_blas; if test "${withval}" = no; then
9.3 4392 withval=$with_blas; R_ARG_USE(blas)
---- configure.ac 2026-01-03 17:00:22.984847292 +0900
-+++ configure.ac 2026-01-03 17:00:22.984847292 +0900
-@@ -33,6 +33,7 @@
+--- configure.ac.orig 2025-04-20 22:15:02.000000000 +0000
++++ configure.ac
+@@ -33,6 +33,7 @@ m4_define([R_VERSION],
AC_INIT([R],[R_VERSION],[https://bugs.r-project.org],[R],[https://www.r-project.org])
AC_CONFIG_SRCDIR([src/include/Defn.h])
AC_CONFIG_AUX_DIR([tools])
@@ -30,7 +35,7 @@ release line #
### * Information on the package.
-@@ -317,6 +318,8 @@
+@@ -322,6 +323,8 @@ AC_ARG_ENABLE([BLAS-shlib],
## As from R 3.2.0 split up -L... and -lR
if test "${want_R_shlib}" = yes; then
LIBR0="-L\"\$(R_HOME)/lib\$(R_ARCH)\""
@@ -39,3 +44,32 @@ release line #
LIBR1=-lR
else
LIBR0=
+@@ -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).
+ ;;
+- *)
++ noboguspaths*)
+ for arg in ${LDFLAGS}; do
+ case "${arg}" in
+ -L*)
+@@ -1864,8 +1867,8 @@ dnl ;;
+ DYLIB_EXT=".dylib"
+ dylib_ldflags="${darwin_dylib_ldflags}"
+ MAJR_VERSION=`echo "${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"
+ ;;
+@@ -2895,7 +2898,7 @@ for arg in ${LDFLAGS} ${FLIBS} ${BLAS_LI
+ case "${arg}" in
+ -L*)
+ lib=`echo ${arg} | sed "s/^-L//"`
+- r_want_lib=true
++ r_want_lib=false
+ ## don't add anything for Darwin
+ case "${host_os}" in darwin*) r_want_lib=false ;; esac
+ ## Do not add non-existent directories.
diff --git a/R/patches/patch-src_extra_xdr_xdr__stdio.c b/R/patches/patch-src_extra_xdr_xdr__stdio.c
index 109db0d745..5408c51967 100644
--- a/R/patches/patch-src_extra_xdr_xdr__stdio.c
+++ b/R/patches/patch-src_extra_xdr_xdr__stdio.c
@@ -1,4 +1,4 @@
-$NetBSD: patch-src_extra_xdr_xdr__stdio.c,v 1.1 2025/01/20 21:26:02 he Exp $
+$NetBSD: patch-src_extra_xdr_xdr__stdio.c,v 1.2 2026/02/16 23:44:02 mef Exp $
Don't do the ntohl() / htonl() dance on NetBSD.
diff --git a/R/patches/patch-src_include_R__ext_Error.h b/R/patches/patch-src_include_R__ext_Error.h
index 547f2dcb40..c2e1365697 100644
--- a/R/patches/patch-src_include_R__ext_Error.h
+++ b/R/patches/patch-src_include_R__ext_Error.h
@@ -1,4 +1,4 @@
-$NetBSD: patch-src_include_R__ext_Error.h,v 1.3 2025/03/02 11:38:51 mef Exp $
+$NetBSD: patch-src_include_R__ext_Error.h,v 1.5 2026/02/16 23:44:02 mef Exp $
Fix building with C++.
diff --git a/R/patches/patch-src_library_grDevices_src_devPS.c b/R/patches/patch-src_library_grDevices_src_devPS.c
index 37a3a42fb7..ead2766d1b 100644
--- a/R/patches/patch-src_library_grDevices_src_devPS.c
+++ b/R/patches/patch-src_library_grDevices_src_devPS.c
@@ -1,4 +1,4 @@
-$NetBSD$
+$NetBSD: patch-src_library_grDevices_src_devPS.c,v 1.1 2026/02/16 23:44:02 mef Exp $
devPS.c: In function 'PDF_endfile':
devPS.c:8173:9: error: implicit declaration of function 'unlink' [-Wimplicit-function-declaration]
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