Update to R-1.6.2

   CHANGES IN R VERSION 1.6.2

BUG FIXES

    o   plot.stepfun() now obeys a `ylim=.' specification.

    o   removeClass() does a better job of removing inheritance
        information.

    o   setIs() will not allow mismatched representations between two
        classes (without an explicit coerce method).

    o   The code underlying polygon drawing contained a memory leak.
        This showed up in persp, but did not affect other graphics
        functions.  It is now possible to draw big DEMs.

    o   logLik.nls() gave wrong df.

    o   rbind() with a mixture of data frames and matrices treated the
        matrices as vectors.

    o   stripchart(method="stack") was not handling missing values.

    o   Arithmetic functions such as log() lost the object bit from
        classed objects if coercion was needed.

    o   exp_rand would go into an infinite loop if unif_rand returned 0.

    o   formatC(x, format="fg") could return exponential format if
        rounding pushed x over a positive power of 10.

    o   attr(x, foo) used partial matching for `foo' (even though not
        documented to do so), and failed to find `foo' if there were
        two or more partial matches before the exact match in the list
        of attributes.

    o   Rdconv now creates direct HTML hyperlinks when linking to
        documentation in the same package.  The code now ensures that
        links which can be resolved within the package are so resolved,
        even when there are possible resolutions in other packages.

    o   If readBin(what=character()) is used incorrectly on a file which
        does not contain C-style character strings, warnings (usually
        many) are now given.

    o   Building libR.so with the zlib in the R sources was not
        finding the local zlib headers.

    o   system(intern=TRUE) has an undocumented line length limit of
        119 chars both on Unix and Windows.  The limit is now 8096 and
        documented.  On Unix (only) every 120th character used to be
        discarded.

    o   plot.POSIX[cl]t were not passing graphics parameters on to
        axis.POSIXct.

    o   On some HP-UX systems, installed scripts were not executable
        when using the BSD-compatible install system program found by
        configure.  We now always use install-sh on HP-UX.

    o   c() was converting NA names to "NA": now proper NA strings are
        used wherever possible.

    o   A typo was causing segfaults when using data.entry under SuSE.

3 files changed, 30 insertions, 25 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index 52d8c6d4260..74064bb28c5 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.41 2002/12/10 11:58:10 markd Exp $
+# $NetBSD: Makefile,v 1.42 2003/01/23 21:24:58 markd Exp $
 
-DISTNAME=		R-1.6.1
+DISTNAME=		R-1.6.2
 CATEGORIES=		math
 MASTER_SITES=		${MASTER_SITE_R_CRAN:=base/}
 EXTRACT_SUFX=		.tgz
diff --git a/math/R/distinfo b/math/R/distinfo
index 9ccff9a060d..6ad99cb4d06 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,10 +1,10 @@
-$NetBSD: distinfo,v 1.11 2002/12/10 11:58:10 markd Exp $
+$NetBSD: distinfo,v 1.12 2003/01/23 21:24:58 markd Exp $
 
-SHA1 (R-1.6.1.tgz) = 6f01abd81cb8ea28205e6511b0ecda826bcbaa84
-Size (R-1.6.1.tgz) = 8633830 bytes
+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) = be0bb888da999cc571f048752204d478efa3d6ac
+SHA1 (patch-ac) = 438bd084536b4f0d2a5ba9eef67f57e0311d7d76
 SHA1 (patch-ad) = b9a08c37baaef8a7169208b758494a077ca531d6
 SHA1 (patch-ae) = 83f0f66d9b135eb81572e7f0be56c02bd95e44d1
 SHA1 (patch-af) = cf00c9bf60bf92aa27c33d750f55184c86be02f1
diff --git a/math/R/patches/patch-ac b/math/R/patches/patch-ac
index 43d17416fe4..1784833afc9 100644
--- a/math/R/patches/patch-ac
+++ b/math/R/patches/patch-ac
@@ -1,8 +1,8 @@
-$NetBSD: patch-ac,v 1.8 2002/12/10 11:58:11 markd Exp $
+$NetBSD: patch-ac,v 1.9 2003/01/23 21:24:58 markd Exp $
 
---- configure.orig	Fri Nov  1 22:48:07 2002
+--- configure.orig	Sat Jan 11 03:52:06 2003
 +++ configure
-@@ -2020,7 +2020,7 @@
+@@ -2095,7 +2095,7 @@
    WANT_R_SHLIB_FALSE=
  fi
  if test "${want_R_shlib}" = yes; then
@@ -11,7 +11,7 @@ $NetBSD: patch-ac,v 1.8 2002/12/10 11:58:11 markd Exp $
  else
    LIBR=
  fi
-@@ -10754,13 +10754,13 @@
+@@ -11123,13 +11123,13 @@
  fi
  
  
@@ -28,8 +28,8 @@ $NetBSD: patch-ac,v 1.8 2002/12/10 11:58:11 markd Exp $
 +LIBS="-ltermcap  $LIBS"
  cat >conftest.$ac_ext <<_ACEOF
  #line $LINENO "configure"
- #include "confdefs.h"
-@@ -10792,33 +10792,33 @@
+ /* confdefs.h.  */
+@@ -11159,34 +11159,34 @@
    ac_status=$?
    echo "$as_me:$LINENO: \$? = $ac_status" >&5
    (exit $ac_status); }; }; then
@@ -37,7 +37,8 @@ $NetBSD: patch-ac,v 1.8 2002/12/10 11:58:11 markd Exp $
 +  ac_cv_lib_termcap_main=yes
  else
    echo "$as_me: failed program was:" >&5
- cat conftest.$ac_ext >&5
+ sed 's/^/| /' conftest.$ac_ext >&5
+ 
 -ac_cv_lib_ncurses_main=no
 +ac_cv_lib_termcap_main=no
  fi
@@ -73,8 +74,8 @@ $NetBSD: patch-ac,v 1.8 2002/12/10 11:58:11 markd Exp $
 +LIBS="-ltermlib  $LIBS"
  cat >conftest.$ac_ext <<_ACEOF
  #line $LINENO "configure"
- #include "confdefs.h"
-@@ -10850,33 +10850,33 @@
+ /* confdefs.h.  */
+@@ -11216,34 +11216,34 @@
    ac_status=$?
    echo "$as_me:$LINENO: \$? = $ac_status" >&5
    (exit $ac_status); }; }; then
@@ -82,7 +83,8 @@ $NetBSD: patch-ac,v 1.8 2002/12/10 11:58:11 markd Exp $
 +  ac_cv_lib_termlib_main=yes
  else
    echo "$as_me: failed program was:" >&5
- cat conftest.$ac_ext >&5
+ sed 's/^/| /' conftest.$ac_ext >&5
+ 
 -ac_cv_lib_termcap_main=no
 +ac_cv_lib_termlib_main=no
  fi
@@ -118,8 +120,8 @@ $NetBSD: patch-ac,v 1.8 2002/12/10 11:58:11 markd Exp $
 +LIBS="-lncurses  $LIBS"
  cat >conftest.$ac_ext <<_ACEOF
  #line $LINENO "configure"
- #include "confdefs.h"
-@@ -10908,23 +10908,23 @@
+ /* confdefs.h.  */
+@@ -11273,24 +11273,24 @@
    ac_status=$?
    echo "$as_me:$LINENO: \$? = $ac_status" >&5
    (exit $ac_status); }; }; then
@@ -127,7 +129,8 @@ $NetBSD: patch-ac,v 1.8 2002/12/10 11:58:11 markd Exp $
 +  ac_cv_lib_ncurses_main=yes
  else
    echo "$as_me: failed program was:" >&5
- cat conftest.$ac_ext >&5
+ sed 's/^/| /' conftest.$ac_ext >&5
+ 
 -ac_cv_lib_termlib_main=no
 +ac_cv_lib_ncurses_main=no
  fi
@@ -150,7 +153,7 @@ $NetBSD: patch-ac,v 1.8 2002/12/10 11:58:11 markd Exp $
  
  fi
  
-@@ -14975,6 +14975,9 @@
+@@ -15432,6 +15432,9 @@
  
  extern void F77_SYMBOL(cftest)(int *a, int *b, double *x, double *y);
  
@@ -160,7 +163,7 @@ $NetBSD: patch-ac,v 1.8 2002/12/10 11:58:11 markd Exp $
  int main () {
    int a[3] = {17, 237, 2000000000}, b[2], res = 0;
    double x[3] = {3.14159265, 123.456789, 2.3e34}, z[3];
-@@ -15063,6 +15066,9 @@
+@@ -15520,6 +15523,9 @@
  
  extern void F77_SYMBOL(cftest)(Rcomplex *x);
  
@@ -170,7 +173,7 @@ $NetBSD: patch-ac,v 1.8 2002/12/10 11:58:11 markd Exp $
  int main () {
      Rcomplex z[3];
  
-@@ -16008,121 +16014,6 @@
+@@ -16510,123 +16516,6 @@
  fi
  
      fi
@@ -208,7 +211,8 @@ $NetBSD: patch-ac,v 1.8 2002/12/10 11:58:11 markd Exp $
 -  eval "r_cv_prog_f77_flag_${ac_safe}=yes"
 -else
 -  echo "$as_me: failed program was:" >&5
--cat conftest.$ac_ext >&5
+-sed 's/^/| /' conftest.$ac_ext >&5
+-
 -eval "r_cv_prog_f77_flag_${ac_safe}=no"
 -fi
 -rm -f conftest.$ac_objext conftest$ac_exeext conftest.$ac_ext
@@ -265,7 +269,8 @@ $NetBSD: patch-ac,v 1.8 2002/12/10 11:58:11 markd Exp $
 -  eval "r_cv_prog_f77_flag_${ac_safe}=yes"
 -else
 -  echo "$as_me: failed program was:" >&5
--cat conftest.$ac_ext >&5
+-sed 's/^/| /' conftest.$ac_ext >&5
+-
 -eval "r_cv_prog_f77_flag_${ac_safe}=no"
 -fi
 -rm -f conftest.$ac_objext conftest$ac_exeext conftest.$ac_ext
@@ -292,7 +297,7 @@ $NetBSD: patch-ac,v 1.8 2002/12/10 11:58:11 markd Exp $
      if test "${GXX}" = yes; then
        ac_safe=`echo "-mieee" | sed 'y%./+-:=%__p___%'`
  echo "$as_me:$LINENO: checking whether ${CXX-c++} accepts -mieee" >&5
-@@ -16862,6 +16753,7 @@
+@@ -17397,6 +17286,7 @@
      fpicflags=
      ;;
    netbsd*)