CVS commit: pkgsrc/math/R

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

Module Name:    pkgsrc
Committed By:   mef
Date:           Sun Mar  2 11:38:51 UTC 2025

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

Log Message:
(math/R) revert to 4.4.2, newone will be put on wip


To generate a diff of this commit:
cvs rdiff -u -r1.266 -r1.267 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.111 -r1.112 pkgsrc/math/R/distinfo
cvs rdiff -u -r0 -r1.12 pkgsrc/math/R/patches/patch-configure.ac
cvs rdiff -u -r0 -r1.3 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:1.266 pkgsrc/math/R/Makefile:1.267
--- pkgsrc/math/R/Makefile:1.266        Sun Mar  2 10:26:38 2025
+++ pkgsrc/math/R/Makefile      Sun Mar  2 11:38:50 2025
@@ -1,10 +1,11 @@
-# $NetBSD: Makefile,v 1.266 2025/03/02 10:26:38 mef Exp $
+# $NetBSD: Makefile,v 1.267 2025/03/02 11:38:50 mef Exp $
 
 #
 # If updating this package, please try to ensure PLIST.Darwin is kept in sync
 # to avoid unnecessarily breaking macOS users.
 #
-DISTNAME=      R-4.4.3
+DISTNAME=      R-4.4.2
+PKGREVISION=   4
 CATEGORIES=    math
 MASTER_SITES=  ${MASTER_SITE_R_CRAN:=base/R-4/}
 

Index: pkgsrc/math/R/distinfo
diff -u pkgsrc/math/R/distinfo:1.111 pkgsrc/math/R/distinfo:1.112
--- pkgsrc/math/R/distinfo:1.111        Sun Mar  2 10:26:38 2025
+++ pkgsrc/math/R/distinfo      Sun Mar  2 11:38:50 2025
@@ -1,10 +1,12 @@
-$NetBSD: distinfo,v 1.111 2025/03/02 10:26:38 mef Exp $
+$NetBSD: distinfo,v 1.112 2025/03/02 11:38:50 mef Exp $
 
-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
+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
 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_library_stats_src_Makefile.in) = 4eb93292858392792c37a706399e2cef91821bbe
 SHA1 (patch-src_main_character.c) = c1be2cae404ecbdd547343b70e9d072e9e1d5549

Added files:

Index: pkgsrc/math/R/patches/patch-configure.ac
diff -u /dev/null pkgsrc/math/R/patches/patch-configure.ac:1.12
--- /dev/null   Sun Mar  2 11:38:51 2025
+++ pkgsrc/math/R/patches/patch-configure.ac    Sun Mar  2 11:38:51 2025
@@ -0,0 +1,133 @@
+$NetBSD: patch-configure.ac,v 1.12 2025/03/02 11:38:51 mef Exp $
+
+Do not include system paths in R_LD_LIBRARY_PATH.
+NetBSD, FreeBSD, DragonFly, Darwin and Solaris fixes
+
+--- configure.ac.orig  2024-03-26 23:02:03.000000000 +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])
++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="${COMPILER_RPATH_FLAG}\"\$(R_HOME)/lib\$(R_ARCH)\" -L\"\$(R_HOME)/lib\$(R_ARCH)\""
+   LIBR1=-lR
+ else
+   LIBR0=
+@@ -898,7 +899,7 @@ case "${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 /dev/null pkgsrc/math/R/patches/patch-src_include_R__ext_Error.h:1.3
--- /dev/null   Sun Mar  2 11:38:51 2025
+++ pkgsrc/math/R/patches/patch-src_include_R__ext_Error.h      Sun Mar  2 11:38:51 2025
@@ -0,0 +1,16 @@
+$NetBSD: patch-src_include_R__ext_Error.h,v 1.3 2025/03/02 11:38:51 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" {
+  * 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