[pkgsrc/trunk]: pkgsrc/math/R Update to R 2.3.1

To: pkgsrc-changes-hg%NetBSD.org@localhost
Subject: [pkgsrc/trunk]: pkgsrc/math/R Update to R 2.3.1
From: markd <markd%pkgsrc.org@localhost>
Date: Thu, 14 Oct 2021 03:36:56 +0000
details:   https://anonhg.NetBSD.org/pkgsrc/rev/5d9a3d1a71b5
branches:  trunk
changeset: 514495:5d9a3d1a71b5
user:      markd <markd%pkgsrc.org@localhost>
date:      Tue Jun 13 12:28:09 2006 +0000

description:
Update to R 2.3.1

This version contains several minor fixups and removes a couple of bad
bugs such as NA-handling of mean() for integer vectors.

Changes 2.3.0
This version contains several changes and additions, mostly incremental.

diffstat:

 math/R/Makefile         |    5 +-
 math/R/distinfo         |   16 +++----
 math/R/patches/patch-aa |   16 +++---
 math/R/patches/patch-ac |  100 +++++++++++++++++++++++++----------------------
 math/R/patches/patch-ad |   20 ++++----
 math/R/patches/patch-ae |   24 -----------
 math/R/patches/patch-at |    8 ---
 7 files changed, 80 insertions(+), 109 deletions(-)

diffs (truncated from 406 to 300 lines):

diff -r 927e3d84e219 -r 5d9a3d1a71b5 math/R/Makefile
--- a/math/R/Makefile   Tue Jun 13 12:16:36 2006 +0000
+++ b/math/R/Makefile   Tue Jun 13 12:28:09 2006 +0000
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.84 2006/06/09 11:15:32 rillig Exp $
+# $NetBSD: Makefile,v 1.85 2006/06/13 12:28:09 markd Exp $
 
-DISTNAME=              R-2.2.1
-PKGREVISION=           3
+DISTNAME=              R-2.3.1
 CATEGORIES=            math
 MASTER_SITES=          ${MASTER_SITE_R_CRAN:=base/R-2/}
 
diff -r 927e3d84e219 -r 5d9a3d1a71b5 math/R/distinfo
--- a/math/R/distinfo   Tue Jun 13 12:16:36 2006 +0000
+++ b/math/R/distinfo   Tue Jun 13 12:28:09 2006 +0000
@@ -1,11 +1,9 @@
-$NetBSD: distinfo,v 1.31 2006/02/26 11:58:25 markd Exp $
+$NetBSD: distinfo,v 1.32 2006/06/13 12:28:09 markd Exp $
 
-SHA1 (R-2.2.1.tar.gz) = 537e0b89b8de55c1156474c76c19c1fcc210f756
-RMD160 (R-2.2.1.tar.gz) = b63b6c5ef1db27a879783460b0ecb6de0d4bba18
-Size (R-2.2.1.tar.gz) = 13665367 bytes
-SHA1 (patch-aa) = 52f7ca0159087a6a5f319dd5476223785fe75a7a
+SHA1 (R-2.3.1.tar.gz) = 62cf87f4a273f17d5a55a5ffaf0bfcdfdae3c03d
+RMD160 (R-2.3.1.tar.gz) = 061a77f25d3b1144aecdce479aa707e7bea21a82
+Size (R-2.3.1.tar.gz) = 14285120 bytes
+SHA1 (patch-aa) = 4041b32f8cc54d6428b47dfac82ceb275bc0ffdf
 SHA1 (patch-ab) = b724b549cd9920865c4d4ae60c71dff48c4c0c06
-SHA1 (patch-ac) = 95888e1a7bbd17a7c258973281adf9c702305673
-SHA1 (patch-ad) = 83c9b046822b1d350daec8739ca4ee2a6b7e1978
-SHA1 (patch-ae) = 4193b3f975bd55ce1d8f720878db31b67ba2d02c
-SHA1 (patch-at) = d972e1072a7f6a30b5fbc2e5fa076bc5bdec5952
+SHA1 (patch-ac) = acf4d4bf230c5128571d19462efd50330eb66812
+SHA1 (patch-ad) = c081d45bdcea860584354b9b35427f70a94f3984
diff -r 927e3d84e219 -r 5d9a3d1a71b5 math/R/patches/patch-aa
--- a/math/R/patches/patch-aa   Tue Jun 13 12:16:36 2006 +0000
+++ b/math/R/patches/patch-aa   Tue Jun 13 12:28:09 2006 +0000
@@ -1,17 +1,17 @@
-$NetBSD: patch-aa,v 1.15 2005/05/02 16:57:19 drochner Exp $
+$NetBSD: patch-aa,v 1.16 2006/06/13 12:28:09 markd Exp $
 
---- configure.ac.orig  2005-04-18 23:30:54.000000000 +0200
+--- configure.ac.orig  2006-05-18 21:13:59.000000000 +1200
 +++ configure.ac
-@@ -306,7 +306,7 @@ AC_ARG_WITH([pcre],
+@@ -361,7 +361,7 @@ AC_ARG_WITH([valgrind-instrumentation],
  ## needs to come after GNOME
  AM_CONDITIONAL(WANT_R_SHLIB, [test "x${want_R_shlib}" = xyes])
  if test "${want_R_shlib}" = yes; then
--  LIBR="-L\$(R_HOME)/lib -lR"
-+  LIBR="-Wl,-R${prefix}/lib/R/lib -L\$(R_HOME)/lib -lR"
+-  LIBR="-L\$(R_HOME)/lib\$(R_ARCH) -lR"
++  LIBR="-Wl,-R${prefix}/lib/R/lib\$(R_ARCH) -L\$(R_HOME)/lib\$(R_ARCH) -lR"
  else
    LIBR=
  fi
-@@ -536,9 +536,9 @@ if test "${use_readline}" = yes; then
+@@ -628,9 +628,9 @@ if test "${use_readline}" = yes; then
    if test "${use_readline}" = no; then
      ## only need ncurses if libreadline is not statically linked against it
      unset ac_cv_lib_readline_rl_callback_read_char
@@ -24,7 +24,7 @@
      AC_CHECK_LIB(readline, rl_callback_read_char)
      use_readline="${ac_cv_lib_readline_rl_callback_read_char}"
    fi
-@@ -681,13 +681,6 @@ case "${host_cpu}" in
+@@ -779,13 +779,6 @@ case "${host_cpu}" in
        R_PROG_CC_FLAG([-ieee_with_inexact],
                       R_SH_VAR_ADD(R_XTRA_CFLAGS, [-ieee_with_inexact]))
      fi
@@ -38,7 +38,7 @@
      if test "${GXX}" = yes; then
        R_PROG_CXX_FLAG([-mieee],
                        R_SH_VAR_ADD(R_XTRA_CXXFLAGS, [-mieee]))
-@@ -986,6 +979,7 @@ case "${host_os}" in
+@@ -1244,6 +1237,7 @@ case "${host_os}" in
      fpicflags=
      ;;
    netbsd*)
diff -r 927e3d84e219 -r 5d9a3d1a71b5 math/R/patches/patch-ac
--- a/math/R/patches/patch-ac   Tue Jun 13 12:16:36 2006 +0000
+++ b/math/R/patches/patch-ac   Tue Jun 13 12:28:09 2006 +0000
@@ -1,38 +1,17 @@
-$NetBSD: patch-ac,v 1.16 2006/02/04 22:25:06 markd Exp $
+$NetBSD: patch-ac,v 1.17 2006/06/13 12:28:09 markd Exp $
 
---- configure.orig     2005-12-16 16:07:00.000000000 +1300
+--- configure.orig     2006-06-01 20:12:54.000000000 +1200
 +++ configure
-@@ -1910,17 +1910,17 @@ fi
- 
- ## R installation directories
- 
--if test -z ${rdocdir}; then
-+if test -z "${rdocdir}"; then
-   rdocdir='${rhome}/doc'
- fi
- 
- 
--if test -z ${rincludedir}; then
-+if test -z "${rincludedir}"; then
-   rincludedir='${rhome}/include'
- fi
- 
- 
--if test -z ${rsharedir}; then
-+if test -z "${rsharedir}"; then
-   rsharedir='${rhome}/share'
- fi
- 
-@@ -2246,7 +2246,7 @@ else
+@@ -2272,7 +2272,7 @@ else
  fi
  
  if test "${want_R_shlib}" = yes; then
--  LIBR="-L\$(R_HOME)/lib -lR"
-+  LIBR="-Wl,-R${prefix}/lib/R/lib -L\$(R_HOME)/lib -lR"
+-  LIBR="-L\$(R_HOME)/lib\$(R_ARCH) -lR"
++  LIBR="-Wl,-R${prefix}/lib/R/lib\$(R_ARCH) -L\$(R_HOME)/lib\$(R_ARCH) -lR"
  else
    LIBR=
  fi
-@@ -6438,7 +6438,7 @@ darwin* | rhapsody*)
+@@ -6580,7 +6580,7 @@ darwin* | rhapsody*)
    lt_cv_deplibs_check_method=pass_all
    ;;
  
@@ -41,7 +20,7 @@
    if echo __ELF__ | $CC -E - | grep __ELF__ > /dev/null; then
      case $host_cpu in
      i*86 )
-@@ -8963,7 +8963,7 @@ if test -z "$aix_libpath"; then aix_libp
+@@ -9101,7 +9101,7 @@ if test -z "$aix_libpath"; then aix_libp
        ;;
  
      # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
@@ -50,7 +29,7 @@
        archive_cmds='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
        hardcode_libdir_flag_spec='-R$libdir'
        hardcode_direct=yes
-@@ -9541,7 +9541,7 @@ kfreebsd*-gnu)
+@@ -9679,7 +9679,7 @@ kfreebsd*-gnu)
    dynamic_linker='GNU ld.so'
    ;;
  
@@ -59,7 +38,7 @@
    objformat=`test -x /usr/bin/objformat && /usr/bin/objformat || echo aout`
    version_type=freebsd-$objformat
    case $version_type in
-@@ -11921,7 +11921,7 @@ if test -z "$aix_libpath"; then aix_libp
+@@ -12060,7 +12060,7 @@ if test -z "$aix_libpath"; then aix_libp
    freebsd-elf*)
      archive_cmds_need_lc_CXX=no
      ;;
@@ -68,7 +47,7 @@
      # FreeBSD 3 and later use GNU C++ and GNU ld with standard ELF
      # conventions
      ld_shlibs_CXX=yes
-@@ -12632,7 +12632,7 @@ echo $ECHO_N "checking for $compiler opt
+@@ -12767,7 +12767,7 @@ echo $ECHO_N "checking for $compiler opt
            ;;
        esac
        ;;
@@ -77,7 +56,7 @@
        # FreeBSD uses GNU C++
        ;;
        hpux9* | hpux10* | hpux11*)
-@@ -13243,7 +13243,7 @@ kfreebsd*-gnu)
+@@ -13378,7 +13378,7 @@ kfreebsd*-gnu)
    dynamic_linker='GNU ld.so'
    ;;
  
@@ -86,7 +65,7 @@
    objformat=`test -x /usr/bin/objformat && /usr/bin/objformat || echo aout`
    version_type=freebsd-$objformat
    case $version_type in
-@@ -15814,7 +15814,7 @@ if test -z "$aix_libpath"; then aix_libp
+@@ -15949,7 +15949,7 @@ if test -z "$aix_libpath"; then aix_libp
        ;;
  
      # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
@@ -95,7 +74,7 @@
        archive_cmds_F77='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
        hardcode_libdir_flag_spec_F77='-R$libdir'
        hardcode_direct_F77=yes
-@@ -16392,7 +16392,7 @@ kfreebsd*-gnu)
+@@ -16527,7 +16527,7 @@ kfreebsd*-gnu)
    dynamic_linker='GNU ld.so'
    ;;
  
@@ -104,7 +83,7 @@
    objformat=`test -x /usr/bin/objformat && /usr/bin/objformat || echo aout`
    version_type=freebsd-$objformat
    case $version_type in
-@@ -18165,7 +18165,7 @@ if test -z "$aix_libpath"; then aix_libp
+@@ -18296,7 +18296,7 @@ if test -z "$aix_libpath"; then aix_libp
        ;;
  
      # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
@@ -113,7 +92,7 @@
        archive_cmds_GCJ='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
        hardcode_libdir_flag_spec_GCJ='-R$libdir'
        hardcode_direct_GCJ=yes
-@@ -18743,7 +18743,7 @@ kfreebsd*-gnu)
+@@ -18874,7 +18874,7 @@ kfreebsd*-gnu)
    dynamic_linker='GNU ld.so'
    ;;
  
@@ -122,7 +101,7 @@
    objformat=`test -x /usr/bin/objformat && /usr/bin/objformat || echo aout`
    version_type=freebsd-$objformat
    case $version_type in
-@@ -21746,13 +21746,13 @@ fi
+@@ -21901,13 +21901,13 @@ fi
      ## only need ncurses if libreadline is not statically linked against it
      unset ac_cv_lib_readline_rl_callback_read_char
  
@@ -131,7 +110,7 @@
 -if test "${ac_cv_lib_ncurses_main+set}" = set; then
 +echo "$as_me:$LINENO: checking for main in -ltermcap" >&5
 +echo $ECHO_N "checking for main in -ltermcap... $ECHO_C" >&6
-+if test "${ac_cv_lib_termcap_main+set}" = set; then
++if test "${ac_cv_lib_termcap+set}" = set; then
    echo $ECHO_N "(cached) $ECHO_C" >&6
  else
    ac_check_lib_save_LIBS=$LIBS
@@ -140,7 +119,7 @@
  cat >conftest.$ac_ext <<_ACEOF
  /* confdefs.h.  */
  _ACEOF
-@@ -21791,35 +21791,35 @@ if { (eval echo "$as_me:$LINENO: \"$ac_l
+@@ -21946,35 +21946,35 @@ if { (eval echo "$as_me:$LINENO: \"$ac_l
    ac_status=$?
    echo "$as_me:$LINENO: \$? = $ac_status" >&5
    (exit $ac_status); }; }; then
@@ -187,7 +166,7 @@
  cat >conftest.$ac_ext <<_ACEOF
  /* confdefs.h.  */
  _ACEOF
-@@ -21858,35 +21858,35 @@ if { (eval echo "$as_me:$LINENO: \"$ac_l
+@@ -22013,35 +22013,35 @@ if { (eval echo "$as_me:$LINENO: \"$ac_l
    ac_status=$?
    echo "$as_me:$LINENO: \$? = $ac_status" >&5
    (exit $ac_status); }; }; then
@@ -234,7 +213,7 @@
  cat >conftest.$ac_ext <<_ACEOF
  /* confdefs.h.  */
  _ACEOF
-@@ -21925,25 +21925,25 @@ if { (eval echo "$as_me:$LINENO: \"$ac_l
+@@ -22080,25 +22080,25 @@ if { (eval echo "$as_me:$LINENO: \"$ac_l
    ac_status=$?
    echo "$as_me:$LINENO: \$? = $ac_status" >&5
    (exit $ac_status); }; }; then
@@ -267,7 +246,7 @@
  
  fi
  
-@@ -27173,6 +27173,7 @@ cat > conftest.c <<EOF
+@@ -27727,6 +27727,7 @@ cat > conftest.c <<EOF
  #else
  # define F77_SYMBOL(x)   x
  #endif
@@ -275,7 +254,7 @@
  int main () {
    exit(0);
  }
-@@ -27243,6 +27244,9 @@ cat > conftest.c <<EOF
+@@ -27796,6 +27797,9 @@ cat > conftest.c <<EOF
  
  extern void F77_SYMBOL(cftest)(int *a, int *b, double *x, double *y);
  
@@ -285,7 +264,7 @@
  int main () {
    int a[3] = {17, 237, 2000000000}, b[2], res = 0;
    double x[3] = {3.14159265, 123.456789, 2.3e34}, z[3];
-@@ -27333,6 +27337,9 @@ typedef struct {
+@@ -27885,6 +27889,9 @@ typedef struct {
  
  extern void F77_SYMBOL(cftest)(Rcomplex *x);
  
@@ -295,7 +274,7 @@
  int main () {
      Rcomplex z[3];
  
-@@ -28170,157 +28177,6 @@ echo "${ECHO_T}no" >&6
+@@ -28277,157 +28284,6 @@ echo "${ECHO_T}no" >&6
  fi
  
      fi
@@ -453,7 +432,16 @@
      if test "${GXX}" = yes; then
        ac_safe=_mieee
  echo "$as_me:$LINENO: checking whether ${CXX-c++} accepts -mieee" >&5
-@@ -29210,7 +29066,7 @@ fi ;;
+@@ -28762,7 +28618,7 @@ _ACEOF
+     if test "${GCC}" = yes; then
+       ## only Apple build of gcc supports (and needs?) -no-cpp-precomp
+       ${CC} --version|grep Apple >/dev/null 2>/dev/null
+-      if test $? == 0; then
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