Update to 3.2.2

Upstream changes:
CHANGES IN R 3.2.2:

  SIGNIFICANT USER-VISIBLE CHANGES:

    * It is now easier to use secure downloads from https:// URLs on
      builds which support them: no longer do non-default options need
      to be selected to do so.  In particular, packages can be
      installed from repositories which offer https:// URLs, and those
      listed by setRepositories() now do so (for some of their
      mirrors).

      Support for https:// URLs is available on Windows, and on other
      platforms if support for libcurl was compiled in and if that
      supports the https protocol (system installations can be expected
      to do).  So https:// support can be expected except on rather old
      OSes (an example being OS X 'Snow Leopard', where a non-system
      version of libcurl can be used).

      (Windows only) The default method for accessing URLs _via_
      download.file() and url() has been changed to be "wininet" using
      Windows API calls.  This changes the way proxies need to be set
      and security settings made: there have been some reports of sites
      being inaccessible under the new default method (but the previous
      methods remain available).

  NEW FEATURES:

    * cmdscale() gets new option list. for increased flexibility when a
      list should be returned.

    * configure now supports texinfo version 6.0, which (unlike the
      change from 4.x to 5.0) is a minor update.  (Wish of PR#16456.)

    * (Non-Windows only) download.file() with default method = "auto"
      now chooses "libcurl" if that is available and a https:// or
      ftps:// URL is used.

    * (Windows only) setInternet2(TRUE) is now the default.  The
      command-line option --internet2 and environment variable
      R_WIN_INTERNET2 are now ignored.

      Thus by default the "internal" method for download.file() and
      url() uses the "wininet" method: to revert to the previous
      default use setInternet2(FALSE).

      This means that https:// can be read by default by
      download.file() (they have been readable by file() and url()
      since R 3.2.0).

      There are implications for how proxies need to be set (see
      ?download.file): also, cacheOK = FALSE is not supported.

    * chooseCRANmirror() and chooseBioCmirror() now offer HTTPS mirrors
      in preference to HTTP mirrors.  This changes the interpretation
      of their ind arguments: see their help pages.

    * capture.output() gets optional arguments type and split to pass
      to sink(), and hence can be used to capture messages.

  C-LEVEL FACILITIES:

    * Header Rconfig.h now defines HAVE_ALLOCA_H if the platform has
      the alloca.h header (it is needed to define alloca on Solaris and
      AIX, at least: see 'Writing R Extensions' for how to use it).

  INSTALLATION and INCLUDED SOFTWARE:

    * The libtool script generated by configure has been modified to
      support FreeBSD >= 10 (PR#16410).

  BUG FIXES:

    * The HTML help page links to demo code failed due to a change in R
      3.2.0.  (PR#16432)

    * If the na.action argument was used in model.frame(), the original
      data could be modified. (PR#16436)

    * getGraphicsEvent() could cause a crash if a graphics window was
      closed while it was in use. (PR#16438)

    * matrix(x, nr, nc, byrow = TRUE) failed if x was an object of type
      "expression".

    * strptime() could overflow the allocated storage on the C stack
      when the timezone had a non-standard format much longer than the
      standard formats. (Part of PR#16328.)

    * options(OutDec = s) now signals a warning (which will become an
      error in the future) when s is not a string with exactly one
      character, as that has been a documented requirement.

    * prettyNum() gains a new option input.d.mark which together with
      other changes, e.g., the default for decimal.mark, fixes some
      format()ting variants with non-default getOption("OutDec") such
      as in PR#16411.

    * download.packages() failed for type equal to either "both" or
      "binary".  (Reported by Dan Tenenbaum.)

    * The dendrogram method of labels() is much more efficient for
      large dendrograms, now using rapply().  (Comment #15 of PR#15215)

    * The "port" algorithm of nls() could give spurious errors.
      (Reported by Radford Neal.)

    * Reference classes that inherited from reference classes in
      another package could invalidate methods of the inherited class.
      Fixing this requires adding the ability for methods to be
      "external", with the object supplied explicitly as the first
      argument, named .self. See "Inter-Package Superclasses" in the
      documentation.

    * readBin() could fail on the SPARC architecture due to alignment
      issues.  (Reported by Radford Neal.)

    * qt(*, df=Inf, ncp=.) now uses the natural qnorm() limit instead
      of returning NaN. (PR#16475)

    * Auto-printing of S3 and S4 values now searches for print() in the
      base namespace and show() in the methods namespace instead of
      searching the global environment.

    * polym() gains a coefs = NULL argument and returns class "poly"
      just like poly() which gets a new simple=FALSE option.  They now
      lead to correct predict()ions, e.g., on subsets of the original
      data.

    * rhyper(nn, <large>) now works correctly. (PR#16489)

    * ttkimage() did not (and could not) work so was removed. Ditto for
      tkimage.cget() and tkimage.configure(). Added two Ttk widgets and
      missing subcommands for Tk's image command: ttkscale(),
      ttkspinbox(), tkimage.delete(), tkimage.height(),
      tkimage.inuse(), tkimage.type(), tkimage.types(),
      tkimage.width(). (PR#15372, PR#16450)

    * getClass("foo") now also returns a class definition when it is
      found in the cache more than once.

4 files changed, 43 insertions, 50 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index 27cbc23153e..ee6690af1c1 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.160 2015/06/30 02:38:52 wen Exp $
+# $NetBSD: Makefile,v 1.161 2015/08/14 12:40:19 wen Exp $
 
-DISTNAME=		R-3.2.1
+DISTNAME=		R-3.2.2
 CATEGORIES=		math
 MASTER_SITES=		${MASTER_SITE_R_CRAN:=base/R-3/}
 
diff --git a/math/R/PLIST b/math/R/PLIST
index 3521ff547fe..6fcb559818e 100644
--- a/math/R/PLIST
+++ b/math/R/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.22 2015/05/26 13:36:57 jperkin Exp $
+@comment $NetBSD: PLIST,v 1.23 2015/08/14 12:40:19 wen Exp $
 bin/R
 bin/Rscript
 info/R-FAQ.info.gz
@@ -36,6 +36,7 @@ lib/R/bin/mkinstalldirs
 lib/R/bin/pager
 lib/R/bin/rtags
 lib/R/doc/AUTHORS
+lib/R/doc/BioC_mirrors.csv
 lib/R/doc/COPYING
 lib/R/doc/COPYRIGHTS
 lib/R/doc/CRAN_mirrors.csv
@@ -363,6 +364,7 @@ lib/R/library/cluster/Meta/links.rds
 lib/R/library/cluster/Meta/nsInfo.rds
 lib/R/library/cluster/Meta/package.rds
 lib/R/library/cluster/NAMESPACE
+lib/R/library/cluster/NEWS.Rd
 lib/R/library/cluster/R/cluster
 lib/R/library/cluster/R/cluster.rdb
 lib/R/library/cluster/R/cluster.rdx
@@ -378,9 +380,12 @@ lib/R/library/cluster/html/00Index.html
 lib/R/library/cluster/html/R.css
 lib/R/library/cluster/libs/cluster.so
 lib/R/library/cluster/po/de/LC_MESSAGES/R-cluster.mo
+lib/R/library/cluster/po/de/LC_MESSAGES/cluster.mo
 lib/R/library/cluster/po/en@quot/LC_MESSAGES/R-cluster.mo
 lib/R/library/cluster/po/en@quot/LC_MESSAGES/cluster.mo
 lib/R/library/cluster/po/fr/LC_MESSAGES/R-cluster.mo
+lib/R/library/cluster/po/ko/LC_MESSAGES/R-cluster.mo
+lib/R/library/cluster/po/ko/LC_MESSAGES/cluster.mo
 lib/R/library/cluster/po/pl/LC_MESSAGES/R-cluster.mo
 lib/R/library/codetools/DESCRIPTION
 lib/R/library/codetools/INDEX
@@ -759,8 +764,6 @@ lib/R/library/mgcv/po/ko/LC_MESSAGES/R-mgcv.mo
 lib/R/library/mgcv/po/ko/LC_MESSAGES/mgcv.mo
 lib/R/library/mgcv/po/pl/LC_MESSAGES/R-mgcv.mo
 lib/R/library/mgcv/po/pl/LC_MESSAGES/mgcv.mo
-lib/R/library/mgcv/po/po/LC_MESSAGES/R-mgcv.mo
-lib/R/library/mgcv/po/po/LC_MESSAGES/mgcv.mo
 lib/R/library/nlme/CITATION
 lib/R/library/nlme/DESCRIPTION
 lib/R/library/nlme/INDEX
diff --git a/math/R/distinfo b/math/R/distinfo
index b64e0cada01..1a81f7b65c5 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.68 2015/07/03 12:45:03 joerg Exp $
+$NetBSD: distinfo,v 1.69 2015/08/14 12:40:19 wen Exp $
 
-SHA1 (R-3.2.1.tar.gz) = 74476c4d356f227bf0f17c8c21e63459861fbc93
-RMD160 (R-3.2.1.tar.gz) = dea095b5c7b32189b6768d5949243bd869564e9f
-Size (R-3.2.1.tar.gz) = 29197870 bytes
-SHA1 (patch-ac) = bf54bef2396714b1d92418d0ad1ecf09610abdfd
+SHA1 (R-3.2.2.tar.gz) = 68c74db1c5a2f2040280a03b8396e4d28a5a7617
+RMD160 (R-3.2.2.tar.gz) = 0e8bf2ecca48f0f2433f6b07f422b7730a76fbb4
+Size (R-3.2.2.tar.gz) = 29772864 bytes
+SHA1 (patch-ac) = 1dc842ca867a1efa4f757ec5cbdca68a6957dd55
 SHA1 (patch-ad) = 0a08f293bc1cdc130047868e5d574c2df1f4c6cf
 SHA1 (patch-src_include_GraphicsBase.h) = 5f999e4d124afd38d5c7e18d936942f2c6f27c86
 SHA1 (patch-src_library_stats_src_Makefile.in) = b468becd011fa4828e50f5d13d700825655c89e8
diff --git a/math/R/patches/patch-ac b/math/R/patches/patch-ac
index c542add0dab..dc2deccd5cd 100644
--- a/math/R/patches/patch-ac
+++ b/math/R/patches/patch-ac
@@ -1,10 +1,10 @@
-$NetBSD: patch-ac,v 1.35 2015/07/03 12:45:03 joerg Exp $
+$NetBSD: patch-ac,v 1.36 2015/08/14 12:40:19 wen Exp $
 
 Do not include system paths in R_LD_LIBRARY_PATH.
 FreeBSD 10 is not FreeBSD 1.
 Fix texi2any version check.
 
---- configure.orig	2015-06-10 22:16:27.000000000 +0000
+--- configure.orig	2015-08-14 19:37:48.000000000 +0000
 +++ configure
 @@ -4012,7 +4012,7 @@ fi
  
@@ -24,25 +24,16 @@ Fix texi2any version check.
    LTOALL=-flto
  fi
  
-@@ -5270,7 +5270,7 @@ if test -z "${texi2any_version_maj}" \
-      || test -z "${texi2any_version_min}"; then
-   r_cv_prog_texi2any_v5=no
+@@ -5272,7 +5272,7 @@ if test -z "${texi2any_version_maj}" \
+ elif test ${texi2any_version_maj} -gt 5; then
+   r_cv_prog_texi2any_v5=yes
  elif test ${texi2any_version_maj} -lt 5 \
 -     || test ${texi2any_version_min} -lt 1; then
 +     || test ${texi2any_version_maj} = 5 -a ${texi2any_version_min} -lt 1; then
    r_cv_prog_texi2any_v5=no
  else
    r_cv_prog_texi2any_v5=yes
-@@ -19921,7 +19921,7 @@ dgux*)
-   shlibpath_var=LD_LIBRARY_PATH
-   ;;
- 
--freebsd1*)
-+freebsd1|freebsd1.*)
-   dynamic_linker=no
-   ;;
- 
-@@ -20514,7 +20514,7 @@ case "${host_os}" in
+@@ -20496,7 +20496,7 @@ case "${host_os}" in
      ## look-up sequence. Such automatic override has proven to break things
      ## like system frameworks (e.g. ImageIO or OpenGL framework).
      ;;
@@ -51,19 +42,19 @@ Fix texi2any version check.
      for arg in ${LDFLAGS}; do
        case "${arg}" in
          -L*)
-@@ -23188,6 +23188,11 @@ fi
+@@ -23170,6 +23170,11 @@ fi
  	  done
  	  ;;
  	-[lLR]*)
-+            case $ac_arg in
-+            -R*)
-+                ac_arg="${wl}$ac_arg"
-+                ;;
-+            esac
++	    case $ac_arg in
++	    -R*)
++		ac_arg="${wl}$ac_arg"
++		;;
++	    esac
  	    ac_exists=false
    for ac_i in $ac_cv_f77_libs; do
      if test x"$ac_arg" = x"$ac_i"; then
-@@ -24153,6 +24158,9 @@ cat > conftest.c <<EOF
+@@ -24135,6 +24140,9 @@ cat > conftest.c <<EOF
  
  extern void F77_SYMBOL(cftest)(int *a, int *b, double *x, double *y);
  
@@ -73,7 +64,7 @@ Fix texi2any version check.
  int main () {
    int a[3] = {17, 237, 2000000000}, b[2], res = 0;
    double x[3] = {3.14159265, 123.456789, 2.3e34}, z[3];
-@@ -24248,6 +24256,9 @@ typedef struct {
+@@ -24230,6 +24238,9 @@ typedef struct {
  
  extern void F77_SYMBOL(cftest)(Rcomplex *x);
  
@@ -83,7 +74,7 @@ Fix texi2any version check.
  int main () {
      Rcomplex z[3];
  
-@@ -26452,12 +26463,12 @@ $as_echo "$as_me: WARNING: Use of flat n
+@@ -26434,12 +26445,12 @@ $as_echo "$as_me: WARNING: Use of flat n
        SHLIB_LIBADD="-lcc_dynamic"
      fi
      ;;
@@ -99,24 +90,23 @@ Fix texi2any version check.
      ;;
    hpux*)
      SHLIB_EXT=".sl"
-@@ -26543,8 +26554,15 @@ $as_echo "$as_me: WARNING: Use of flat n
+@@ -26525,8 +26536,14 @@ $as_echo "$as_me: WARNING: Use of flat n
      fcpicflags=
      ;;
    netbsd*)
-+     fpicflags="-fPIC"
-+     case "${host_cpu}" in
-+       powerpc*)
-+        cpicflags="-fPIC"
-+        ;;
-+     esac
-+
++	fpicflags="-fPIC"
++	case "${host_cpu}" in
++	  powerpc*)
++	  cpicflags="-fPIC"
++	  ;;
++	esac
      if ${CPP} - -dM < /dev/null | grep __ELF__ >/dev/null ; then
 -      main_ldflags="-export-dynamic"
 +      main_ldflags="${wl}-export-dynamic"
        shlib_ldflags="-shared"
      else
        shlib_ldflags="-Bshareable"
-@@ -26566,22 +26584,22 @@ $as_echo "$as_me: WARNING: Use of flat n
+@@ -26548,22 +26565,22 @@ $as_echo "$as_me: WARNING: Use of flat n
    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.
@@ -143,7 +133,7 @@ Fix texi2any version check.
        cpicflags="-KPIC"
        if test "`basename ${CXX}`" = "CC" ; then
          ## Forte version 7 needs -lCstd: Forte 6 does not.
-@@ -26642,7 +26660,7 @@ fi
+@@ -26624,7 +26641,7 @@ fi
  : ${CPICFLAGS="${cpicflags}"}
  if test -z "${CPICFLAGS}"; then
    case "${host_os}" in
@@ -152,7 +142,7 @@ Fix texi2any version check.
        ;;
      *)
        { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: I could not determine CPICFLAGS." >&5
-@@ -27338,6 +27356,14 @@ _ACEOF
+@@ -27320,6 +27337,14 @@ _ACEOF
  ## Cygwin has rintl but not nearbyintl
  for ac_func in expm1 hypot log1p log1pl log2 log10 nearbyint nearbyintl powl rint rintl
  do
@@ -167,7 +157,7 @@ Fix texi2any version check.
  as_ac_Symbol=`$as_echo "ac_cv_have_decl_$ac_func" | $as_tr_sh`
  { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $ac_func exists and is declared" >&5
  $as_echo_n "checking whether $ac_func exists and is declared... " >&6; }
-@@ -27347,24 +27373,12 @@ else
+@@ -27329,24 +27354,12 @@ else
    cat confdefs.h - <<_ACEOF >conftest.$ac_ext
  /* end confdefs.h.  */
  #include <math.h>
@@ -190,11 +180,11 @@ Fix texi2any version check.
 -
 -  ;
 -  return 0;
-+  return $ac_func($args);
++  return $ac_func($args);;
  }
  _ACEOF
  if ac_fn_c_try_link "$LINENO"; then :
-@@ -30274,6 +30288,15 @@ cat > conftest.c <<EOF
+@@ -30256,6 +30269,15 @@ cat > conftest.c <<EOF
  #endif
  extern void F77_SYMBOL(test1)(int *iflag);
  
@@ -210,7 +200,7 @@ Fix texi2any version check.
  int main () {
    int iflag;
    F77_SYMBOL(test1)(&iflag);
-@@ -30338,6 +30361,14 @@ else
+@@ -30320,6 +30342,14 @@ else
  #else
  # define F77_SYMBOL(x)   x
  #endif
@@ -225,7 +215,7 @@ Fix texi2any version check.
  void F77_SYMBOL(xerbla)(char *srname, int *info)
  {}
  void blas_set () {
-@@ -38953,7 +38984,7 @@ case "${host_os}" in
+@@ -38927,7 +38957,7 @@ case "${host_os}" in
      r_ld_library_defaults="/usr/lib64:/lib64:/usr/lib:/lib"
      ;;
    solaris*)