CVS commit: pkgsrc/math/R

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/math/R
From: "Makoto Fujiwara" <mef%netbsd.org@localhost>
Date: Sat, 3 Jan 2026 09:17:26 +0000

Module Name:    pkgsrc
Committed By:   mef
Date:           Sat Jan  3 09:17:26 UTC 2026

Modified Files:
        pkgsrc/math/R: Makefile distinfo
        pkgsrc/math/R/patches: patch-configure.ac
            patch-src_include_R__ext_Error.h

Log Message:
(math/R) Updated 4.4.2 to 4.4.3, based on wip/R

The usual commit log was once made on 2025/03/02 as follows:
----------------------------
revision 1.266
date: 2025-03-02 19:26:38 +0900;  author: mef;  state: Exp;  lines: +2 -3;  commitid: 2z43hv4v7E22OtLF;
(math/R) Updated 4.4.2 to 4.4.3

CHANGES IN R 4.4.3:
   .....
----------------------------
The problem on above commit may be turned out as one char typo:

-+AC_CONFIG_MACRO_DIR([m4])
++AC_CONFIG_MACRO_DIRS([m4])

really sorry


To generate a diff of this commit:
cvs rdiff -u -r1.273 -r1.274 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.112 -r1.113 pkgsrc/math/R/distinfo
cvs rdiff -u -r1.12 -r1.13 pkgsrc/math/R/patches/patch-configure.ac
cvs rdiff -u -r1.3 -r1.4 \
    pkgsrc/math/R/patches/patch-src_include_R__ext_Error.h

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:1.273 pkgsrc/math/R/Makefile:1.274
--- pkgsrc/math/R/Makefile:1.273        Thu Oct 23 20:38:13 2025
+++ pkgsrc/math/R/Makefile      Sat Jan  3 09:17:26 2026
@@ -1,11 +1,10 @@
-# $NetBSD: Makefile,v 1.273 2025/10/23 20:38:13 wiz Exp $
+# $NetBSD: Makefile,v 1.274 2026/01/03 09:17:26 mef Exp $
 
 #
 # If updating this package, please try to ensure PLIST.Darwin is kept in sync
 # to avoid unnecessarily breaking macOS users.
 #
-DISTNAME=      R-4.4.2
-PKGREVISION=   10
+DISTNAME=      R-4.4.3
 CATEGORIES=    math
 MASTER_SITES=  ${MASTER_SITE_R_CRAN:=base/R-4/}
 
@@ -16,6 +15,10 @@ LICENSE=     gnu-gpl-v2
 
 USE_GCC_RUNTIME=       yes
 
+# https://cran.r-project.org/doc/manuals/r-release/NEWS.pdf
+# above line mentions c23 as default compiler for R, but c23 (gcc15) is N/A ?
+# USE_CC_FEATURES+=    c23
+
 BUILD_TARGET=          all info
 INSTALL_TARGET=                install install-info
 TEST_TARGET=           check

Index: pkgsrc/math/R/distinfo
diff -u pkgsrc/math/R/distinfo:1.112 pkgsrc/math/R/distinfo:1.113
--- pkgsrc/math/R/distinfo:1.112        Sun Mar  2 11:38:50 2025
+++ pkgsrc/math/R/distinfo      Sat Jan  3 09:17:26 2026
@@ -1,12 +1,12 @@
-$NetBSD: distinfo,v 1.112 2025/03/02 11:38:50 mef Exp $
+$NetBSD: distinfo,v 1.113 2026/01/03 09:17:26 mef Exp $
 
-BLAKE2s (R-4.4.2.tar.gz) = eb8c3d41ba6d0e12401f03410d2c8bb37dc3344989824c990f9a33f08ebb6c5c
-SHA512 (R-4.4.2.tar.gz) = b29d82242f70487f52849a5726610c03dffa4e54f1a32a9f3f76784fcf61f91d5c40cddee1029eeb9c9837ff26f382f348e8518dd68c84e9fc2192b981013d9a
-Size (R-4.4.2.tar.gz) = 37582785 bytes
-SHA1 (patch-configure.ac) = 7a62031864a9cef7b40278a7579293469fba7446
+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-configure.ac) = 61904b7918019204634d61bce2421c01c81ed640
 SHA1 (patch-m4_R.m4) = 3e1d390d8aa9895aee7cb479ddab371d82562b88
 SHA1 (patch-src_extra_xdr_xdr__mem.c) = 2e607b070db8b24a6ad5501e9c7c1549bf1b1d82
 SHA1 (patch-src_extra_xdr_xdr__stdio.c) = e4d8ace08ad282f44113941dd6a3b194769b8167
-SHA1 (patch-src_include_R__ext_Error.h) = bc55a8bba6bf931e3f6794577e63bfafdfc740cf
+SHA1 (patch-src_include_R__ext_Error.h) = fc91727ed68172489667c9b19a8c51f972ed3fd9
 SHA1 (patch-src_library_stats_src_Makefile.in) = 4eb93292858392792c37a706399e2cef91821bbe
 SHA1 (patch-src_main_character.c) = c1be2cae404ecbdd547343b70e9d072e9e1d5549

Index: pkgsrc/math/R/patches/patch-configure.ac
diff -u pkgsrc/math/R/patches/patch-configure.ac:1.12 pkgsrc/math/R/patches/patch-configure.ac:1.13
--- pkgsrc/math/R/patches/patch-configure.ac:1.12       Sun Mar  2 11:38:51 2025
+++ pkgsrc/math/R/patches/patch-configure.ac    Sat Jan  3 09:17:26 2026
@@ -1,133 +1,41 @@
-$NetBSD: patch-configure.ac,v 1.12 2025/03/02 11:38:51 mef Exp $
+$NetBSD: patch-configure.ac,v 1.13 2026/01/03 09:17:26 mef Exp $
 
-Do not include system paths in R_LD_LIBRARY_PATH.
-NetBSD, FreeBSD, DragonFly, Darwin and Solaris fixes
+on NetBSD/amd64 9.4: getting
 
---- configure.ac.orig  2024-03-26 23:02:03.000000000 +0000
-+++ configure.ac
-@@ -33,6 +33,7 @@ m4_define([R_VERSION],
+autoreconf: running: libtoolize --copy --force
+libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'tools'.
+libtoolize: copying file 'tools/ltmain.sh'
+libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac,
+ ...
+ ...
+loading site script './config.site'
+loading build-specific script './config.site'
+./configure: 4429: Syntax error: Word "blas" unexpected (expecting ")")
+*** Error code 2
+
+
+configure(s) generated are different on 10.99.12 and 9.4
+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 @@
  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])
++AC_CONFIG_MACRO_DIRS([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 "${host_os}" = "linux-musl"; then
-   AC_DEFINE(OS_MUSL, 1, [Define if running on Linux-musl])
- fi
- 
-@@ -316,7 +317,7 @@ AC_ARG_ENABLE([BLAS-shlib],
- 
+@@ -317,6 +318,8 @@
  ## As from R 3.2.0 split up -L... and -lR
  if test "${want_R_shlib}" = yes; then
--  LIBR0="-L\"\$(R_HOME)/lib\$(R_ARCH)\""
-+  LIBR0="${COMPILER_RPATH_FLAG}\"\$(R_HOME)/lib\$(R_ARCH)\" -L\"\$(R_HOME)/lib\$(R_ARCH)\""
+   LIBR0="-L\"\$(R_HOME)/lib\$(R_ARCH)\""
++  LIBR0="-Wl,-R${prefix}/lib/R/lib\$(R_ARCH) -L\"\$(R_HOME)/lib\$(R_ARCH)\""                                                                                       |
++  LIBR0="${COMPILER_RPATH_FLAG}\"\$(R_HOME)/lib\$(R_ARCH)\" -L\"\$(R_HOME)/lib\$(R_ARCH)\""                                                                        |
    LIBR1=-lR
  else
    LIBR0=
-@@ -898,7 +899,7 @@ case "${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`

Index: pkgsrc/math/R/patches/patch-src_include_R__ext_Error.h
diff -u pkgsrc/math/R/patches/patch-src_include_R__ext_Error.h:1.3 pkgsrc/math/R/patches/patch-src_include_R__ext_Error.h:1.4
--- pkgsrc/math/R/patches/patch-src_include_R__ext_Error.h:1.3  Sun Mar  2 11:38:51 2025
+++ pkgsrc/math/R/patches/patch-src_include_R__ext_Error.h      Sat Jan  3 09:17:26 2026
@@ -1,15 +1,15 @@
-$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 1.4 2026/01/03 09:17:26 mef 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" {
+--- src/include/R_ext/Error.h.orig     2025-01-19 08:15:01.000000000 +0900
++++ src/include/R_ext/Error.h  2026-01-03 08:54:10.539893482 +0900
+@@ -45,7 +45,8 @@
   * 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) || \
+-#elif (defined(__clang__) && defined(__STDC_VERSION__) && __STDC_VERSION__ >= 202301L)
++#elif (defined(__clang__) && defined(__STDC_VERSION__) && __STDC_VERSION__ >= 202301L) || \
 +      (defined(__cplusplus) && __cplusplus >= 201103L)
  # define NORET [[noreturn]]
  #elif defined(__STDC_VERSION__) && __STDC_VERSION__ >= 201102L

Prev by Date: CVS commit: pkgsrc/doc
Next by Date: CVS commit: pkgsrc/doc
Previous by Thread: CVS commit: pkgsrc/doc
Next by Thread: CVS commit: pkgsrc/doc
Indexes:

Home | Main Index | Thread Index | Old Index