[pkgsrc/trunk]: pkgsrc/math/R Update R to 1.8.1.

To: pkgsrc-changes-hg%NetBSD.org@localhost
Subject: [pkgsrc/trunk]: pkgsrc/math/R Update R to 1.8.1.
From: markd <markd%pkgsrc.org@localhost>
Date: Wed, 13 Oct 2021 23:11:28 +0000
details:   https://anonhg.NetBSD.org/pkgsrc/rev/ccaec1c9205c
branches:  trunk
changeset: 463992:ccaec1c9205c
user:      markd <markd%pkgsrc.org@localhost>
date:      Wed Dec 03 12:05:18 2003 +0000

description:
Update R to 1.8.1.

Changes since 1.6.2

Many new features.
Language changes.
Additional standard package 'mle'.
Some old features deprecated or defunct.
Many many bug fixes.

Update to 1.8.0 from Ray Brownrigg in private communication, cleaned up
and updated to 1.8.1 by me.

diffstat:

 math/R/Makefile           |    8 +-
 math/R/Makefile.extension |    4 +-
 math/R/buildlink2.mk      |    4 +-
 math/R/distinfo           |   41 +++++----
 math/R/patches/patch-aa   |   31 ++-----
 math/R/patches/patch-ab   |   22 +++-
 math/R/patches/patch-ac   |  186 +++++++--------------------------------------
 math/R/patches/patch-ad   |    8 +-
 math/R/patches/patch-ae   |   28 +++--
 math/R/patches/patch-af   |   28 +++--
 math/R/patches/patch-ag   |   28 +++--
 math/R/patches/patch-ah   |   28 +++--
 math/R/patches/patch-ai   |   28 +++--
 math/R/patches/patch-aj   |   28 +++--
 math/R/patches/patch-ak   |   28 +++--
 math/R/patches/patch-al   |   28 +++--
 math/R/patches/patch-am   |   28 +++--
 math/R/patches/patch-an   |   28 +++--
 math/R/patches/patch-ao   |   28 +++--
 math/R/patches/patch-ap   |   28 +++--
 math/R/patches/patch-aq   |   28 +++--
 math/R/patches/patch-ar   |   21 +++++
 22 files changed, 320 insertions(+), 369 deletions(-)

diffs (truncated from 987 to 300 lines):

diff -r 7f263d8683a0 -r ccaec1c9205c math/R/Makefile
--- a/math/R/Makefile   Wed Dec 03 12:00:09 2003 +0000
+++ b/math/R/Makefile   Wed Dec 03 12:05:18 2003 +0000
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.44 2003/07/17 21:47:15 grant Exp $
+# $NetBSD: Makefile,v 1.45 2003/12/03 12:05:18 markd Exp $
 
-DISTNAME=              R-1.6.2
+DISTNAME=              R-1.8.1
 CATEGORIES=            math
 MASTER_SITES=          ${MASTER_SITE_R_CRAN:=base/}
 EXTRACT_SUFX=          .tgz
@@ -13,11 +13,14 @@
 NOT_FOR_PLATFORM=      NetBSD-1.[0-4]*-alpha NetBSD-1.5-alpha \
                        NetBSD-1.5.*-alpha NetBSD-1.5[A-U]-alpha
 
+TEST_TARGET=           check
 USE_BUILDLINK2=                # defined
 USE_X11=               # defined
 USE_PERL5=             # defined
 USE_GMAKE=             # defined
 USE_GNU_READLINE=      # uses callback interface
+USE_MAKEINFO=          # defined
+TEXINFO_REQD=          4.0
 
 GNU_CONFIGURE=         # defined
 CONFIGURE_ARGS+=       --enable-R-shlib
@@ -110,6 +113,7 @@
        ${ECHO} "@exec R CMD ${PERL5} %D/lib/R/share/perl/build-help.pl --htmllists 2>/dev/null" >> ${PLIST_SRC}
        ${ECHO} "@exec ${CAT} %D/lib/R/library/*/CONTENTS > %D/lib/R/doc/html/search/index.txt 2>/dev/null" >> ${PLIST_SRC}
 
+.include "../../devel/pcre/buildlink2.mk"
 .include "../../devel/readline/buildlink2.mk"
 .include "../../devel/zlib/buildlink2.mk"
 .include "../../graphics/jpeg/buildlink2.mk"
diff -r 7f263d8683a0 -r ccaec1c9205c math/R/Makefile.extension
--- a/math/R/Makefile.extension Wed Dec 03 12:00:09 2003 +0000
+++ b/math/R/Makefile.extension Wed Dec 03 12:05:18 2003 +0000
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile.extension,v 1.4 2003/03/29 12:41:38 jmmv Exp $
+# $NetBSD: Makefile.extension,v 1.5 2003/12/03 12:05:18 markd Exp $
 #
 # This Makefile fragment is included by packages for R library packages.
 #
@@ -15,7 +15,7 @@
 DIST_SUBDIR?=          R
 CATEGORIES+=           math
 
-R_DEPENDS?=            R>=1.4.1nb2
+R_DEPENDS?=            R>=1.7.0
 DEPENDS+=               ${R_DEPENDS}:../../math/R
 
 NO_BUILD=              YES
diff -r 7f263d8683a0 -r ccaec1c9205c math/R/buildlink2.mk
--- a/math/R/buildlink2.mk      Wed Dec 03 12:00:09 2003 +0000
+++ b/math/R/buildlink2.mk      Wed Dec 03 12:05:18 2003 +0000
@@ -1,4 +1,4 @@
-# $NetBSD: buildlink2.mk,v 1.2 2003/03/14 19:37:48 jlam Exp $
+# $NetBSD: buildlink2.mk,v 1.3 2003/12/03 12:05:18 markd Exp $
 #
 # This Makefile fragment is included by packages that use the R shared library.
 #
@@ -7,7 +7,7 @@
 R_BUILDLINK2_MK=       # defined
 
 BUILDLINK_PACKAGES+=           R
-BUILDLINK_DEPENDS.R?=          R>=1.6.1
+BUILDLINK_DEPENDS.R?=          R>=1.7.0
 BUILDLINK_PKGSRCDIR.R?=                ../../math/R
 
 EVAL_PREFIX+=                  BUILDLINK_PREFIX.R=R
diff -r 7f263d8683a0 -r ccaec1c9205c math/R/distinfo
--- a/math/R/distinfo   Wed Dec 03 12:00:09 2003 +0000
+++ b/math/R/distinfo   Wed Dec 03 12:05:18 2003 +0000
@@ -1,21 +1,22 @@
-$NetBSD: distinfo,v 1.12 2003/01/23 21:24:58 markd Exp $
+$NetBSD: distinfo,v 1.13 2003/12/03 12:05:18 markd Exp $
 
-SHA1 (R-1.6.2.tgz) = bc7527d856e7a1d1dcbb2bfc71606d6bb9111bcd
-Size (R-1.6.2.tgz) = 8659106 bytes
-SHA1 (patch-aa) = 8ec7504d5c08e4258b0b1a433aed8760f630089e
-SHA1 (patch-ab) = a3bd4d27abbc7f26e223aaa1e559ccfc0e363c39
-SHA1 (patch-ac) = 438bd084536b4f0d2a5ba9eef67f57e0311d7d76
-SHA1 (patch-ad) = b9a08c37baaef8a7169208b758494a077ca531d6
-SHA1 (patch-ae) = 83f0f66d9b135eb81572e7f0be56c02bd95e44d1
-SHA1 (patch-af) = cf00c9bf60bf92aa27c33d750f55184c86be02f1
-SHA1 (patch-ag) = a4312c4f64ca0af1ee425ce25bef5fe06212e580
-SHA1 (patch-ah) = 37e2b7466ced465a412d1792fbcd17159f09aabf
-SHA1 (patch-ai) = 8a815753bbc2de4785b19ee3b3c2df4c9ca26578
-SHA1 (patch-aj) = 0a75114a5b34739f05418739c65e44e87ce024fb
-SHA1 (patch-ak) = 737a2329d14f5c6e516cf44cf66af421fc9a4b1c
-SHA1 (patch-al) = a2c582dd463bd85c6670ca981214c4a27bbdca5f
-SHA1 (patch-am) = 8ac2214f490f48f6cc780608b99cb07896a7fd7d
-SHA1 (patch-an) = dff4e97ca33fab0937c70b8dc3a8bcda799a4ab9
-SHA1 (patch-ao) = b94e2b6c8ad844be16f3dbcb9f96f7ba4f71094f
-SHA1 (patch-ap) = b2a273fe3865e8a7413762defb95966f54dd8de8
-SHA1 (patch-aq) = 36c7ad5c8ad0db9f9d879a196dfe9fb1dcc452d8
+SHA1 (R-1.8.1.tgz) = 397511dcef3a04ebb67ef23988f5c32eee72fe95
+Size (R-1.8.1.tgz) = 9407628 bytes
+SHA1 (patch-aa) = c81131e2a8601ff061502e72a9f322d955dfe72c
+SHA1 (patch-ab) = 192044af2d9cd73f19e8324384cab91635e27067
+SHA1 (patch-ac) = 83f261aa8a538ad013505582c821c459d4628f08
+SHA1 (patch-ad) = 69706964d6bc13e40ade009cbf1bb61d80d4fb36
+SHA1 (patch-ae) = 917fe5d509bcef59e18215c4a4ad3662694fca37
+SHA1 (patch-af) = da90dd523784806ffc71617760c71b4dbf0dfbe3
+SHA1 (patch-ag) = 108795b4e679aa5149df1dcb3d3b7cf40c5b3f86
+SHA1 (patch-ah) = b986ada9088875748361dc1750812e53d1900260
+SHA1 (patch-ai) = 2f7fc15dcc08659dfb6c2fef097af7f86bb17e67
+SHA1 (patch-aj) = b23b6f4d113cf2a49881bff6c34b0408c961499c
+SHA1 (patch-ak) = 5927f451f05674d431687c93dca4c452e59889da
+SHA1 (patch-al) = 9081ae2e771fcede31b085097f41334030d36ebe
+SHA1 (patch-am) = 47c47fdc12e7c771eb29c066575c666eaec96870
+SHA1 (patch-an) = e45ce6861ec7e35e02faf46c95863803783f2bda
+SHA1 (patch-ao) = c99629da4329e67d1adbb48cd89a50531743d63f
+SHA1 (patch-ap) = b75680bae0d75f417c74d2137ba4b43ec1428131
+SHA1 (patch-aq) = 512d7613bbba00c0cb3e4543812f734159e12a92
+SHA1 (patch-ar) = 5cc4a77c253a77a564433187babb0135ccb84eaf
diff -r 7f263d8683a0 -r ccaec1c9205c math/R/patches/patch-aa
--- a/math/R/patches/patch-aa   Wed Dec 03 12:00:09 2003 +0000
+++ b/math/R/patches/patch-aa   Wed Dec 03 12:05:18 2003 +0000
@@ -1,8 +1,8 @@
-$NetBSD: patch-aa,v 1.10 2002/12/10 11:58:11 markd Exp $
+$NetBSD: patch-aa,v 1.11 2003/12/03 12:05:18 markd Exp $
 
---- configure.ac.orig  Mon Oct 21 22:27:50 2002
+--- configure.ac.orig  2003-09-17 11:01:04.000000000 +1200
 +++ configure.ac
-@@ -148,7 +148,7 @@
+@@ -134,7 +134,7 @@ AC_ARG_ENABLE([R-shlib],
  [want_R_shlib=no])
  AM_CONDITIONAL(WANT_R_SHLIB, [test "x${want_R_shlib}" = xyes])
  if test "${want_R_shlib}" = yes; then
@@ -11,34 +11,21 @@
  else
    LIBR=
  fi
-@@ -412,9 +412,9 @@ AC_SUBST(LIBM)
- ## AC_CHECK_LIBM computes LIBM but does not add to LIBS, hence we do
- ## the following as well.
- AC_CHECK_LIB(m, sin)
--AC_CHECK_LIB(ncurses, main, [],
--             AC_CHECK_LIB(termcap, main, [],
--                          AC_CHECK_LIB(termlib, main)))
-+AC_CHECK_LIB(termcap, main, [],
-+             AC_CHECK_LIB(termlib, main, [],
-+                          AC_CHECK_LIB(ncurses, main)))
- AC_CHECK_LIB(dl, dlopen)
- 
- ## Readline.
-@@ -555,13 +555,6 @@ case "${host_cpu}" in
+@@ -592,13 +592,6 @@ case "${host_cpu}" in
        R_PROG_CC_FLAG([-ieee_with_inexact],
-                      [R_XTRA_CFLAGS="${R_XTRA_CFLAGS} -ieee_with_inexact"])
+                      R_SH_VAR_ADD(R_XTRA_CFLAGS, [-ieee_with_inexact]))
      fi
 -    if test "${G77}" = yes; then
 -      R_PROG_F77_FLAG([-mieee],
--                      [R_XTRA_FFLAGS="${R_XTRA_FFLAGS} -mieee"])
+-                      R_SH_VAR_ADD(R_XTRA_FFLAGS, [-mieee]))
 -    else
 -      R_PROG_F77_FLAG([-fpe3],
--                      [R_XTRA_FFLAGS="${R_XTRA_FFLAGS} -fpe3"])
+-                      R_SH_VAR_ADD(R_XTRA_FFLAGS, [-fpe3]))
 -    fi
      if test "${GXX}" = yes; then
        R_PROG_CXX_FLAG([-mieee],
-                       [R_XTRA_CXXFLAGS="${R_XTRA_CXXFLAGS} -mieee"])
-@@ -821,6 +814,7 @@ case "${host_os}" in
+                       R_SH_VAR_ADD(R_XTRA_CXXFLAGS, [-mieee]))
+@@ -891,6 +884,7 @@ case "${host_os}" in
      fpicflags=
      ;;
    netbsd*)
diff -r 7f263d8683a0 -r ccaec1c9205c math/R/patches/patch-ab
--- a/math/R/patches/patch-ab   Wed Dec 03 12:00:09 2003 +0000
+++ b/math/R/patches/patch-ab   Wed Dec 03 12:05:18 2003 +0000
@@ -1,8 +1,16 @@
-$NetBSD: patch-ab,v 1.14 2002/12/10 11:58:11 markd Exp $
+$NetBSD: patch-ab,v 1.15 2003/12/03 12:05:18 markd Exp $
 
---- aclocal.m4.orig    Mon Oct 21 22:28:00 2002
+--- aclocal.m4.orig    2003-09-27 18:08:39.000000000 +1200
 +++ aclocal.m4
-@@ -522,6 +522,9 @@
+@@ -572,6 +572,7 @@ ${F77} ${FFLAGS} -c conftestf.f 1>&AS_ME
+ #else
+ # define F77_SYMBOL(x)   x
+ #endif
++int MAIN__ () { return 0; }
+ int main () {
+   exit(0);
+ }
+@@ -633,6 +634,9 @@ ${F77} ${FFLAGS} -c conftestf.f 1>&AS_ME
  
  extern void F77_SYMBOL(cftest)(int *a, int *b, double *x, double *y);
  
@@ -12,13 +20,13 @@
  int main () {
    int a[3] = {17, 237, 2000000000}, b[2], res = 0;
    double x[3] = {3.14159265, 123.456789, 2.3e34}, z[3];
-@@ -602,6 +605,9 @@
- } Rcomplex;
+@@ -714,6 +718,9 @@ typedef struct {
  
  extern void F77_SYMBOL(cftest)(Rcomplex *x);
-+
+ 
 +int MAIN_ () { return 0; }
 +int MAIN__ () { return 0; }
- 
++
  int main () {
      Rcomplex z[3];
+     
diff -r 7f263d8683a0 -r ccaec1c9205c math/R/patches/patch-ac
--- a/math/R/patches/patch-ac   Wed Dec 03 12:00:09 2003 +0000
+++ b/math/R/patches/patch-ac   Wed Dec 03 12:05:18 2003 +0000
@@ -1,8 +1,8 @@
-$NetBSD: patch-ac,v 1.9 2003/01/23 21:24:58 markd Exp $
+$NetBSD: patch-ac,v 1.10 2003/12/03 12:05:18 markd Exp $
 
---- configure.orig     Sat Jan 11 03:52:06 2003
+--- configure.orig     2003-10-08 22:59:51.000000000 +1300
 +++ configure
-@@ -2095,7 +2095,7 @@
+@@ -2108,7 +2108,7 @@ else
    WANT_R_SHLIB_FALSE=
  fi
  if test "${want_R_shlib}" = yes; then
@@ -11,149 +11,15 @@
  else
    LIBR=
  fi
-@@ -11123,13 +11123,13 @@
- fi
- 
- 
--echo "$as_me:$LINENO: checking for main in -lncurses" >&5
--echo $ECHO_N "checking for main in -lncurses... $ECHO_C" >&6
--if test "${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
-   echo $ECHO_N "(cached) $ECHO_C" >&6
- else
-   ac_check_lib_save_LIBS=$LIBS
--LIBS="-lncurses  $LIBS"
-+LIBS="-ltermcap  $LIBS"
- cat >conftest.$ac_ext <<_ACEOF
- #line $LINENO "configure"
- /* confdefs.h.  */
-@@ -11159,34 +11159,34 @@
-   ac_status=$?
-   echo "$as_me:$LINENO: \$? = $ac_status" >&5
-   (exit $ac_status); }; }; then
--  ac_cv_lib_ncurses_main=yes
-+  ac_cv_lib_termcap_main=yes
- else
-   echo "$as_me: failed program was:" >&5
- sed 's/^/| /' conftest.$ac_ext >&5
- 
--ac_cv_lib_ncurses_main=no
-+ac_cv_lib_termcap_main=no
- fi
- rm -f conftest.$ac_objext conftest$ac_exeext conftest.$ac_ext
- LIBS=$ac_check_lib_save_LIBS
- fi
--echo "$as_me:$LINENO: result: $ac_cv_lib_ncurses_main" >&5
--echo "${ECHO_T}$ac_cv_lib_ncurses_main" >&6
--if test $ac_cv_lib_ncurses_main = yes; then
-+echo "$as_me:$LINENO: result: $ac_cv_lib_termcap_main" >&5
-+echo "${ECHO_T}$ac_cv_lib_termcap_main" >&6
-+if test $ac_cv_lib_termcap_main = yes; then
-   cat >>confdefs.h <<_ACEOF
--#define HAVE_LIBNCURSES 1
-+#define HAVE_LIBTERMCAP 1
- _ACEOF
- 
--  LIBS="-lncurses $LIBS"
-+  LIBS="-ltermcap $LIBS"
- 
- else
- 
--echo "$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
-+echo "$as_me:$LINENO: checking for main in -ltermlib" >&5
-+echo $ECHO_N "checking for main in -ltermlib... $ECHO_C" >&6
-+if test "${ac_cv_lib_termlib_main+set}" = set; then
-   echo $ECHO_N "(cached) $ECHO_C" >&6
- else
-   ac_check_lib_save_LIBS=$LIBS
--LIBS="-ltermcap  $LIBS"
-+LIBS="-ltermlib  $LIBS"
- cat >conftest.$ac_ext <<_ACEOF
- #line $LINENO "configure"
- /* confdefs.h.  */
-@@ -11216,34 +11216,34 @@
-   ac_status=$?
-   echo "$as_me:$LINENO: \$? = $ac_status" >&5
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