Changes 2.11.0:

* Packages must have been installed under R >= 2.10.0, as the
  current help system is the only one now supported.
* A port to 64-bit Windows is now available as well as binary package
  repositiories: see the 'R Administration and Installation Manual'.
* Argument matching for primitive functions is now done in the same way
  as for interpreted functions except for the deliberate exceptions
	call switch .C .Fortran .Call .External
  all of which use positional matching for their first argument,
  and also some internal-use-only primitives.
* The default device for command-line R at the console on Mac OS X
  is now quartz() and not X11().

New features
* The 'open' modes for connections are now interpreted more consistently.
* R CMD INSTALL now uses the internal untar() in package utils.
* help(try.all.packages = TRUE) is much faster.
* R CMD check has a new option '--timings' to record per-example timings
  in file <pkg>.Rcheck/<pkg>-Ex.timings.
* The TRE library has been updated to version 0.8.0 (minor bugfixes).
More...

6 files changed, 36 insertions, 180 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index bd2fc71e033..f2134d390b6 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.106 2010/02/09 07:02:53 adam Exp $
+# $NetBSD: Makefile,v 1.107 2010/05/06 07:33:40 adam Exp $
 
-DISTNAME=		R-2.10.1
+DISTNAME=		R-2.11.0
 CATEGORIES=		math
 MASTER_SITES=		${MASTER_SITE_R_CRAN:=base/R-2/}
 
@@ -62,6 +62,7 @@ CONFIGURE_ENV+=		lt_cv_path_LD=${LD:Q}
 CONFIGURE_ENV+=		lt_cv_path_SED=${TOOLS_SED}
 CONFIGURE_ENV+=		ac_cv_path_R_GZIPCMD=${TOOLS_GZIP_CMD}
 CONFIGURE_ENV+=		ac_cv_path_R_UNZIPCMD=${TOOLS_PATH.unzip}
+CONFIGURE_ENV+=		r_cv_prog_f77_flag_mieee=no
 
 # Package assumes it can append to files (specifically DESCRIPTION) that have
 # been installed SHAREMODE
diff --git a/math/R/PLIST b/math/R/PLIST
index ba2cfa627fe..dccdae46331 100644
--- a/math/R/PLIST
+++ b/math/R/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.10 2009/12/11 18:53:40 adam Exp $
+@comment $NetBSD: PLIST,v 1.11 2010/05/06 07:33:40 adam Exp $
 bin/R
 bin/Rscript
 lib/R/COPYING
@@ -1037,6 +1037,13 @@ lib/R/library/survival/help/survival.rdb
 lib/R/library/survival/help/survival.rdx
 lib/R/library/survival/html/00Index.html
 lib/R/library/survival/libs/survival.so
+lib/R/library/survival/noweb/Makefile
+lib/R/library/survival/noweb/Readme
+lib/R/library/survival/noweb/main.Rnw
+lib/R/library/survival/noweb/noweb.sty
+lib/R/library/survival/noweb/nwmac.tex
+lib/R/library/survival/noweb/predict.coxph.Rnw
+lib/R/library/survival/noweb/residuals.survreg.Rnw
 lib/R/library/tcltk/DESCRIPTION
 lib/R/library/tcltk/INDEX
 lib/R/library/tcltk/Meta/Rd.rds
diff --git a/math/R/distinfo b/math/R/distinfo
index 1278784497a..8b599b847c3 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.42 2010/02/09 07:02:53 adam Exp $
+$NetBSD: distinfo,v 1.43 2010/05/06 07:33:41 adam Exp $
 
-SHA1 (R-2.10.1.tar.gz) = f5b1969fde3642c233f5198e44a7bf17a7b85ab6
-RMD160 (R-2.10.1.tar.gz) = 7acf060192f205da4731d0ea3c2cc318b65b7e91
-Size (R-2.10.1.tar.gz) = 19705604 bytes
-SHA1 (patch-ab) = c70f9f94bace4129b81f19d8802ae1de50c9f24e
-SHA1 (patch-ac) = eda258c5be9630fac013ea1f5a6785de299c1509
-SHA1 (patch-ad) = 5c6fd9f68d8fe4a12147d94c07590025427878fc
+SHA1 (R-2.11.0.tar.gz) = 86af359879afaf18bf0cd9ca36f2957d7b146ba3
+RMD160 (R-2.11.0.tar.gz) = 358d5ba19bd534e9f5be56f517bd217c235599dc
+Size (R-2.11.0.tar.gz) = 19779908 bytes
+SHA1 (patch-ab) = 629c8d5f9d2278c97f48fb55c0e5172a0aea58b2
+SHA1 (patch-ac) = 53b4e331d8887a469e74662c1a19ad5571ed72d6
+SHA1 (patch-ad) = 43ae23bd0815986c3bac661bd3354cd96b3e54e4
diff --git a/math/R/patches/patch-ab b/math/R/patches/patch-ab
index 46312c6cbc6..a83a065ee02 100644
--- a/math/R/patches/patch-ab
+++ b/math/R/patches/patch-ab
@@ -1,8 +1,8 @@
-$NetBSD: patch-ab,v 1.19 2009/12/11 18:53:40 adam Exp $
+$NetBSD: patch-ab,v 1.20 2010/05/06 07:33:41 adam Exp $
 
---- src/include/Defn.h.orig	2009-09-30 04:05:04.000000000 +0200
+--- src/include/Defn.h.orig	2010-03-25 08:31:54.000000000 +0000
 +++ src/include/Defn.h
-@@ -1232,7 +1232,7 @@ extern char *locale2charset(const char *
+@@ -1243,7 +1243,7 @@ extern char *locale2charset(const char *
  # ifdef HAVE_ALLOCA_H
  #  include <alloca.h>
  # endif
diff --git a/math/R/patches/patch-ac b/math/R/patches/patch-ac
index ae37314ba55..d8d71dacdba 100644
--- a/math/R/patches/patch-ac
+++ b/math/R/patches/patch-ac
@@ -1,8 +1,8 @@
-$NetBSD: patch-ac,v 1.24 2009/12/11 18:53:40 adam Exp $
+$NetBSD: patch-ac,v 1.25 2010/05/06 07:33:41 adam Exp $
 
---- configure.orig	2009-10-15 04:06:36.000000000 +0200
+--- configure.orig	2010-03-31 22:10:52.000000000 +0000
 +++ configure
-@@ -2719,7 +2719,7 @@ fi
+@@ -3755,7 +3755,7 @@ fi
  
  
  if test "${want_R_shlib}" = yes; then
@@ -11,7 +11,7 @@ $NetBSD: patch-ac,v 1.24 2009/12/11 18:53:40 adam Exp $
  else
    LIBR=
  fi
-@@ -28544,6 +28544,7 @@ cat > conftest.c <<EOF
+@@ -23591,6 +23591,7 @@ cat > conftest.c <<EOF
  #else
  # define F77_SYMBOL(x)   x
  #endif
@@ -19,7 +19,7 @@ $NetBSD: patch-ac,v 1.24 2009/12/11 18:53:40 adam Exp $
  int main () {
    exit(0);
  }
-@@ -28621,6 +28622,9 @@ cat > conftest.c <<EOF
+@@ -23667,6 +23668,9 @@ cat > conftest.c <<EOF
  
  extern void F77_SYMBOL(cftest)(int *a, int *b, double *x, double *y);
  
@@ -29,7 +29,7 @@ $NetBSD: patch-ac,v 1.24 2009/12/11 18:53:40 adam Exp $
  int main () {
    int a[3] = {17, 237, 2000000000}, b[2], res = 0;
    double x[3] = {3.14159265, 123.456789, 2.3e34}, z[3];
-@@ -28718,6 +28722,9 @@ typedef struct {
+@@ -23762,6 +23766,9 @@ typedef struct {
  
  extern void F77_SYMBOL(cftest)(Rcomplex *x);
  
@@ -39,159 +39,7 @@ $NetBSD: patch-ac,v 1.24 2009/12/11 18:53:40 adam Exp $
  int main () {
      Rcomplex z[3];
  
-@@ -29802,151 +29809,6 @@ echo "${ECHO_T}no" >&6; }
- fi
- 
-     fi
--    if test "${G77}" = yes; then
--      ac_safe=_mieee
--{ echo "$as_me:$LINENO: checking whether ${F77} accepts -mieee" >&5
--echo $ECHO_N "checking whether ${F77} accepts -mieee... $ECHO_C" >&6; }
--if { as_var=r_cv_prog_f77_flag_${ac_safe}; eval "test \"\${$as_var+set}\" = set"; }; then
--  echo $ECHO_N "(cached) $ECHO_C" >&6
--else
--  ac_ext=f
--ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5'
--ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
--ac_compiler_gnu=$ac_cv_f77_compiler_gnu
--
--r_save_FFLAGS="${FFLAGS}"
--FFLAGS="${FFLAGS} -mieee"
--cat >conftest.$ac_ext <<_ACEOF
--      program main
--
--      end
--_ACEOF
--rm -f conftest.$ac_objext conftest$ac_exeext
--if { (ac_try="$ac_link"
--case "(($ac_try" in
--  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
--  *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
--  (eval "$ac_link") 2>conftest.er1
--  ac_status=$?
--  grep -v '^ *+' conftest.er1 >conftest.err
--  rm -f conftest.er1
--  cat conftest.err >&5
--  echo "$as_me:$LINENO: \$? = $ac_status" >&5
--  (exit $ac_status); } && {
--	 test -z "$ac_f77_werror_flag" ||
--	 test ! -s conftest.err
--       } && test -s conftest$ac_exeext &&
--       $as_test_x conftest$ac_exeext; then
--  eval "r_cv_prog_f77_flag_${ac_safe}=yes"
--else
--  echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
--	eval "r_cv_prog_f77_flag_${ac_safe}=no"
--fi
--
--rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
--      conftest$ac_exeext conftest.$ac_ext
--FFLAGS="${r_save_FFLAGS}"
--ac_ext=c
--ac_cpp='$CPP $CPPFLAGS'
--ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
--ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
--ac_compiler_gnu=$ac_cv_c_compiler_gnu
--
--
--fi
--
--if eval "test \"`echo '$r_cv_prog_f77_flag_'$ac_safe`\" = yes"; then
--  { echo "$as_me:$LINENO: result: yes" >&5
--echo "${ECHO_T}yes" >&6; }
--  separator=""
--test -z "${separator}" && separator=" "
--if test -z "${R_XTRA_FFLAGS}"; then
--  R_XTRA_FFLAGS="-mieee"
--else
--  R_XTRA_FFLAGS="${R_XTRA_FFLAGS}${separator}-mieee"
--fi
--else
--  { echo "$as_me:$LINENO: result: no" >&5
--echo "${ECHO_T}no" >&6; }
--fi
--
--    else
--      ac_safe=_fpe3
--{ echo "$as_me:$LINENO: checking whether ${F77} accepts -fpe3" >&5
--echo $ECHO_N "checking whether ${F77} accepts -fpe3... $ECHO_C" >&6; }
--if { as_var=r_cv_prog_f77_flag_${ac_safe}; eval "test \"\${$as_var+set}\" = set"; }; then
--  echo $ECHO_N "(cached) $ECHO_C" >&6
--else
--  ac_ext=f
--ac_compile='$F77 -c $FFLAGS conftest.$ac_ext >&5'
--ac_link='$F77 -o conftest$ac_exeext $FFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
--ac_compiler_gnu=$ac_cv_f77_compiler_gnu
--
--r_save_FFLAGS="${FFLAGS}"
--FFLAGS="${FFLAGS} -fpe3"
--cat >conftest.$ac_ext <<_ACEOF
--      program main
--
--      end
--_ACEOF
--rm -f conftest.$ac_objext conftest$ac_exeext
--if { (ac_try="$ac_link"
--case "(($ac_try" in
--  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
--  *) ac_try_echo=$ac_try;;
--esac
--eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
--  (eval "$ac_link") 2>conftest.er1
--  ac_status=$?
--  grep -v '^ *+' conftest.er1 >conftest.err
--  rm -f conftest.er1
--  cat conftest.err >&5
--  echo "$as_me:$LINENO: \$? = $ac_status" >&5
--  (exit $ac_status); } && {
--	 test -z "$ac_f77_werror_flag" ||
--	 test ! -s conftest.err
--       } && test -s conftest$ac_exeext &&
--       $as_test_x conftest$ac_exeext; then
--  eval "r_cv_prog_f77_flag_${ac_safe}=yes"
--else
--  echo "$as_me: failed program was:" >&5
--sed 's/^/| /' conftest.$ac_ext >&5
--
--	eval "r_cv_prog_f77_flag_${ac_safe}=no"
--fi
--
--rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
--      conftest$ac_exeext conftest.$ac_ext
--FFLAGS="${r_save_FFLAGS}"
--ac_ext=c
--ac_cpp='$CPP $CPPFLAGS'
--ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
--ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
--ac_compiler_gnu=$ac_cv_c_compiler_gnu
--
--
--fi
--
--if eval "test \"`echo '$r_cv_prog_f77_flag_'$ac_safe`\" = yes"; then
--  { echo "$as_me:$LINENO: result: yes" >&5
--echo "${ECHO_T}yes" >&6; }
--  separator=""
--test -z "${separator}" && separator=" "
--if test -z "${R_XTRA_FFLAGS}"; then
--  R_XTRA_FFLAGS="-fpe3"
--else
--  R_XTRA_FFLAGS="${R_XTRA_FFLAGS}${separator}-fpe3"
--fi
--else
--  { echo "$as_me:$LINENO: result: no" >&5
--echo "${ECHO_T}no" >&6; }
--fi
--
--    fi
-     if test "${GXX}" = yes; then
-       ac_safe=_mieee
- { echo "$as_me:$LINENO: checking whether ${CXX-c++} accepts -mieee" >&5
-@@ -31453,7 +31315,7 @@ echo "$as_me: WARNING: Use of flat names
+@@ -25918,7 +25925,7 @@ $as_echo "$as_me: WARNING: Use of flat n
        SHLIB_LIBADD="-lcc_dynamic"
      fi
      ;;
@@ -200,7 +48,7 @@ $NetBSD: patch-ac,v 1.24 2009/12/11 18:53:40 adam Exp $
      ## Only sure for FreeBSD 3 and above.
      main_ldflags="-export-dynamic"
      shlib_ldflags="-shared"
-@@ -31542,6 +31404,12 @@ echo "$as_me: WARNING: Use of flat names
+@@ -26007,6 +26014,12 @@ $as_echo "$as_me: WARNING: Use of flat n
      fcpicflags=
      ;;
    netbsd*)
@@ -213,7 +61,7 @@ $NetBSD: patch-ac,v 1.24 2009/12/11 18:53:40 adam Exp $
      if ${CPP} - -dM < /dev/null | grep __ELF__ >/dev/null ; then
        main_ldflags="-export-dynamic"
        shlib_ldflags="-shared"
-@@ -31641,7 +31509,7 @@ fi
+@@ -26104,7 +26117,7 @@ fi
  : ${FPICFLAGS="${fpicflags}"}
  if test -z "${FPICFLAGS}"; then
    case "${host_os}" in
@@ -221,8 +69,8 @@ $NetBSD: patch-ac,v 1.24 2009/12/11 18:53:40 adam Exp $
 +    aix*|cygwin*|irix*|mingw*|osf*|darwin*)
        ;;
      *)
-       { echo "$as_me:$LINENO: WARNING: I could not determine FPICFLAGS." >&5
-@@ -38017,6 +37885,15 @@ cat > conftest.c <<EOF
+       { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: I could not determine FPICFLAGS." >&5
+@@ -29156,6 +29169,15 @@ cat > conftest.c <<EOF
  #endif
  extern void F77_SYMBOL(test1)(int *iflag);
  
@@ -238,7 +86,7 @@ $NetBSD: patch-ac,v 1.24 2009/12/11 18:53:40 adam Exp $
  int main () {
    int iflag;
    F77_SYMBOL(test1)(&iflag);
-@@ -38084,6 +37961,14 @@ else
+@@ -29223,6 +29245,14 @@ else
  #else
  # define F77_SYMBOL(x)   x
  #endif
diff --git a/math/R/patches/patch-ad b/math/R/patches/patch-ad
index 3352006c663..843d4671fa3 100644
--- a/math/R/patches/patch-ad
+++ b/math/R/patches/patch-ad
@@ -1,8 +1,8 @@
-$NetBSD: patch-ad,v 1.13 2009/12/11 18:53:40 adam Exp $
+$NetBSD: patch-ad,v 1.14 2010/05/06 07:33:41 adam Exp $
 
---- src/main/Makefile.in.orig	2009-10-14 04:05:03.000000000 +0200
+--- src/main/Makefile.in.orig	2010-03-25 08:32:02.000000000 +0000
 +++ src/main/Makefile.in
-@@ -97,13 +97,13 @@ EXTRA_STATIC_LIBS = \
+@@ -96,13 +96,13 @@ EXTRA_STATIC_LIBS = \
    $(R_ZLIBS) $(R_BZLIBS) $(R_PCRE) $(R_TRE) $(R_XDR) $(R_XZ) $(R_LIBINTL)
  STATIC_LIBS = $(MAIN_LIBS) $(EXTRA_STATIC_LIBS)