Update to R 3.2.4

3.2.4
NEW FEATURES

install.packages() and related functions now give a more informative
warning when an attempt is made to install a base package.

summary(x) now prints with less rounding when x contains infinite values.

provideDimnames() gets an optional unique argument.

shQuote() gains type = "cmd2" for quoting in cmd.exe in Windows.

The data.frame method of rbind() gains an optional argument stringsAsFactors
(instead of only depending on getOption("stringsAsFactors")).

smooth(x, *) now also works for long vectors.

tools::texi2dvi() has a workaround for problems with the texi2dvi script
supplied by texinfo 6.1.

It extracts more error messages from the LaTeX logs when in emulation mode.

DEPRECATED AND DEFUNCT

Use of SUPPORT_OPENMP from header ‘Rconfig.h’ is deprecated in favour of
the standard OpenMP define _OPENMP.

(This has been the recommendation in the manual for a while now.)

The make macro AWK which is long unused by R itself but recorded in file
‘etc/Makeconf’ is deprecated and will be removed in R 3.3.0.

The C header file ‘S.h’ is no longer documented: its use should be
replaced by ‘R.h’.

3.2.3

NEW FEATURES

Some recently-added Windows time zone names have been added to the
conversion table used to convert these to Olson names. (Including
those relating to changes for Russia in Oct 2014, as in PR#16503.)

(Windows) Compatibility information has been added to the manifests
for ‘Rgui.exe’, ‘Rterm.exe’ and ‘Rscript.exe’. This should allow
win.version() and Sys.info() to report the actual Windows version up
to Windows 10.

Windows "wininet" FTP first tries EPSV / PASV mode rather than only
using active mode (reported by Dan Tenenbaum).

which.min(x) and which.max(x) may be much faster for logical and integer
x and now also work for long vectors.

The ‘emulation’ part of tools::texi2dvi() has been somewhat enhanced,
including supporting quiet = TRUE. It can be selected by texi2dvi =
"emulation".

(Windows) MiKTeX removed its texi2dvi.exe command in Sept 2015:
tools::texi2dvi() tries texify.exe if it is not found.

(Windows only) Shortcuts for printing and saving have been added to
menus in Rgui.exe.

loess(..., iterTrace=TRUE) now provides diagnostics for robustness
iterations, and the print() method for summary(<loess>) shows slightly
more.

The included version of PCRE has been updated to 8.38, a bug-fix release.

View() now displays nested data frames in a more friendly way.

5 files changed, 49 insertions, 58 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index c74acfe2665..07aee98e0d8 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.164 2016/02/25 15:26:55 jperkin Exp $
+# $NetBSD: Makefile,v 1.165 2016/04/13 21:04:04 markd Exp $
 
-DISTNAME=		R-3.2.2
+DISTNAME=		R-3.2.4
 CATEGORIES=		math
 MASTER_SITES=		${MASTER_SITE_R_CRAN:=base/R-3/}
 
diff --git a/math/R/PLIST b/math/R/PLIST
index 6fcb559818e..04d7ed60747 100644
--- a/math/R/PLIST
+++ b/math/R/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.23 2015/08/14 12:40:19 wen Exp $
+@comment $NetBSD: PLIST,v 1.24 2016/04/13 21:04:04 markd Exp $
 bin/R
 bin/Rscript
 info/R-FAQ.info.gz
@@ -203,6 +203,7 @@ lib/R/library/Matrix/Copyrights
 lib/R/library/Matrix/DESCRIPTION
 lib/R/library/Matrix/Doxyfile
 lib/R/library/Matrix/INDEX
+lib/R/library/Matrix/LICENCE
 lib/R/library/Matrix/Meta/Rd.rds
 lib/R/library/Matrix/Meta/data.rds
 lib/R/library/Matrix/Meta/hsearch.rds
diff --git a/math/R/distinfo b/math/R/distinfo
index 7daf6f222db..01893eaaf1e 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,11 +1,11 @@
-$NetBSD: distinfo,v 1.71 2016/02/19 21:57:42 jperkin Exp $
+$NetBSD: distinfo,v 1.72 2016/04/13 21:04:04 markd Exp $
 
-SHA1 (R-3.2.2.tar.gz) = 68c74db1c5a2f2040280a03b8396e4d28a5a7617
-RMD160 (R-3.2.2.tar.gz) = 0e8bf2ecca48f0f2433f6b07f422b7730a76fbb4
-SHA512 (R-3.2.2.tar.gz) = 71ba470875262b9f00fb6970f209788df4dad30e0a28373b824b60d8bc6401afb7786e65387663c6490c7ddcd2bfd7f808a270a3e63238f3d7565d5f93607138
-Size (R-3.2.2.tar.gz) = 29772864 bytes
-SHA1 (patch-ac) = b6fc368714a3c962d343d68dedda2347063b6c83
-SHA1 (patch-ad) = 0a08f293bc1cdc130047868e5d574c2df1f4c6cf
+SHA1 (R-3.2.4.tar.gz) = 632664b3caa8d39f5fe6ac2ee9611b0f89ad6ed9
+RMD160 (R-3.2.4.tar.gz) = 1bf1a6cd2974a543914d06e7914510fef9c5690d
+SHA512 (R-3.2.4.tar.gz) = a74f01a9b47437feb81520c10936a6f2bc7700900730ec87b7f1442ee90bcf1d7aac9ef3345aa046c0566f1920f114da0a616c5f355b1e8480dc01e311476cbf
+Size (R-3.2.4.tar.gz) = 29879523 bytes
+SHA1 (patch-ac) = 4ef1aa72f338d769ff2fbad36a1337e2947a4d18
+SHA1 (patch-ad) = 2f1ef086bfb4213ed2911830419714903038e8a3
 SHA1 (patch-src_include_GraphicsBase.h) = 5f999e4d124afd38d5c7e18d936942f2c6f27c86
 SHA1 (patch-src_library_stats_src_Makefile.in) = b468becd011fa4828e50f5d13d700825655c89e8
 SHA1 (patch-src_main_character.c) = bd6e9b5b633d86c913c98d9d87c66f982d1ca258
diff --git a/math/R/patches/patch-ac b/math/R/patches/patch-ac
index c5dc97d4705..4278c74ab7c 100644
--- a/math/R/patches/patch-ac
+++ b/math/R/patches/patch-ac
@@ -1,12 +1,12 @@
-$NetBSD: patch-ac,v 1.37 2016/02/19 21:57:42 jperkin Exp $
+$NetBSD: patch-ac,v 1.38 2016/04/13 21:04:04 markd Exp $
 
 Do not include system paths in R_LD_LIBRARY_PATH.
 FreeBSD 10 is not FreeBSD 1.
 Fix texi2any version check.
 
---- configure.orig	2015-08-13 09:21:16.000000000 +0000
+--- configure.orig	2016-03-02 23:16:44.000000000 +0000
 +++ configure
-@@ -4012,7 +4012,7 @@ fi
+@@ -4023,7 +4023,7 @@ fi
  
  ## As from R 3.2.0 split up -L... and -lR
  if test "${want_R_shlib}" = yes; then
@@ -15,7 +15,7 @@ Fix texi2any version check.
    LIBR1=-lR
  else
    LIBR0=
-@@ -4078,7 +4078,7 @@ fi
+@@ -4088,7 +4088,7 @@ fi
  if test "x${want_lto}" != xno; then
    LTO=-flto
  fi
@@ -24,7 +24,7 @@ Fix texi2any version check.
    LTOALL=-flto
  fi
  
-@@ -5272,7 +5272,7 @@ if test -z "${texi2any_version_maj}" \
+@@ -5297,7 +5297,7 @@ if test -z "${texi2any_version_maj}" \
  elif test ${texi2any_version_maj} -gt 5; then
    r_cv_prog_texi2any_v5=yes
  elif test ${texi2any_version_maj} -lt 5 \
@@ -33,16 +33,16 @@ Fix texi2any version check.
    r_cv_prog_texi2any_v5=no
  else
    r_cv_prog_texi2any_v5=yes
-@@ -20496,7 +20496,7 @@ case "${host_os}" in
-     ## look-up sequence. Such automatic override has proven to break things
-     ## like system frameworks (e.g. ImageIO or OpenGL framework).
+@@ -20523,7 +20523,7 @@ case "${host_os}" in
+     ## Not so bad in later versions of Darwin,
+     ## where DYLD_FALLBACK_LIBRARY_PATH is used (see below).
      ;;
 -  *)
 +  donotuse*)
      for arg in ${LDFLAGS}; do
        case "${arg}" in
          -L*)
-@@ -23170,6 +23170,11 @@ fi
+@@ -23200,6 +23200,11 @@ fi
  	  done
  	  ;;
  	-[lLR]*)
@@ -54,7 +54,7 @@ Fix texi2any version check.
  	    ac_exists=false
    for ac_i in $ac_cv_f77_libs; do
      if test x"$ac_arg" = x"$ac_i"; then
-@@ -24135,6 +24140,9 @@ cat > conftest.c <<EOF
+@@ -24165,6 +24170,9 @@ cat > conftest.c <<EOF
  
  extern void F77_SYMBOL(cftest)(int *a, int *b, double *x, double *y);
  
@@ -64,7 +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];
-@@ -24230,6 +24238,9 @@ typedef struct {
+@@ -24260,6 +24268,9 @@ typedef struct {
  
  extern void F77_SYMBOL(cftest)(Rcomplex *x);
  
@@ -74,39 +74,29 @@ Fix texi2any version check.
  int main () {
      Rcomplex z[3];
  
-@@ -26434,12 +26445,12 @@ $as_echo "$as_me: WARNING: Use of flat n
+@@ -26468,7 +26479,7 @@ $as_echo "$as_me: WARNING: Use of flat n
        SHLIB_LIBADD="-lcc_dynamic"
      fi
      ;;
 -  freebsd*)
--    main_ldflags="-export-dynamic"
 +  freebsd*|dragonfly*)
-+    main_ldflags="${wl}-export-dynamic"
-     shlib_ldflags="-shared"
-     ;;
-   gnu*)				# GNU Hurd
--    main_ldflags="-export-dynamic"
-+    main_ldflags="${wl}-export-dynamic"
-     ;;
-   hpux*)
-     SHLIB_EXT=".sl"
-@@ -26525,8 +26536,14 @@ $as_echo "$as_me: WARNING: Use of flat n
-     fcpicflags=
+     ## maybe this needs to depend on the compiler:
+     ## -export-dynamic used to work, but does not with clang.
+     ## Seems FreeBSD has used the GNU linker since at least 3.0 (Oct 1998)
+@@ -26563,6 +26574,12 @@ $as_echo "$as_me: WARNING: Use of flat n
      ;;
    netbsd*)
-+	fpicflags="-fPIC"
-+	case "${host_cpu}" in
-+	  powerpc*)
-+	  cpicflags="-fPIC"
-+	  ;;
-+	esac
+     ## See the comments about FreeBSD
++      fpicflags="-fPIC"
++      case "${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"
+       main_ldflags="-Wl,--export-dynamic"
        shlib_ldflags="-shared"
-     else
-       shlib_ldflags="-Bshareable"
-@@ -26548,22 +26565,22 @@ $as_echo "$as_me: WARNING: Use of flat n
+@@ -26589,22 +26606,22 @@ $as_echo "$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.
@@ -133,7 +123,7 @@ Fix texi2any version check.
        cpicflags="-KPIC"
        if test "`basename ${CXX}`" = "CC" ; then
          ## Forte version 7 needs -lCstd: Forte 6 does not.
-@@ -26624,7 +26641,7 @@ fi
+@@ -26665,7 +26682,7 @@ fi
  : ${CPICFLAGS="${cpicflags}"}
  if test -z "${CPICFLAGS}"; then
    case "${host_os}" in
@@ -142,7 +132,7 @@ Fix texi2any version check.
        ;;
      *)
        { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: I could not determine CPICFLAGS." >&5
-@@ -26723,10 +26740,10 @@ case "${host_os}" in
+@@ -26765,10 +26782,10 @@ case "${host_os}" in
      DYLIB_EXT=".dylib"
      dylib_ldflags="${darwin_dylib_ldflags}"
      MAJR_VERSION=`echo "${PACKAGE_VERSION}" | sed  -e "s/[\.][1-9]$/.0/"`
@@ -156,8 +146,8 @@ Fix texi2any version check.
      ;;
    hpux*)
      ## Needs to avoid embedding a relative path ../../../bin.
-@@ -27320,6 +27337,14 @@ _ACEOF
- ## Cygwin has rintl but not nearbyintl
+@@ -27390,6 +27407,14 @@ _ACEOF
+ ## Cygwin had rintl but not nearbyintl
  for ac_func in expm1 hypot log1p log1pl log2 log10 nearbyint nearbyintl powl rint rintl
  do
 +case $ac_func in
@@ -171,7 +161,7 @@ Fix texi2any version check.
  as_ac_Symbol=`$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 $ac_func exists and is declared... " >&6; }
-@@ -27329,24 +27354,12 @@ else
+@@ -27399,24 +27424,12 @@ else
    cat confdefs.h - <<_ACEOF >conftest.$ac_ext
  /* end confdefs.h.  */
  #include <math.h>
@@ -198,7 +188,7 @@ Fix texi2any version check.
  }
  _ACEOF
  if ac_fn_c_try_link "$LINENO"; then :
-@@ -30256,6 +30269,15 @@ cat > conftest.c <<EOF
+@@ -30326,6 +30339,15 @@ cat > conftest.c <<EOF
  #endif
  extern void F77_SYMBOL(test1)(int *iflag);
  
@@ -214,7 +204,7 @@ Fix texi2any version check.
  int main () {
    int iflag;
    F77_SYMBOL(test1)(&iflag);
-@@ -30320,6 +30342,14 @@ else
+@@ -30390,6 +30412,14 @@ else
  #else
  # define F77_SYMBOL(x)   x
  #endif
@@ -229,12 +219,12 @@ Fix texi2any version check.
  void F77_SYMBOL(xerbla)(char *srname, int *info)
  {}
  void blas_set () {
-@@ -38927,7 +38957,7 @@ case "${host_os}" in
+@@ -39021,7 +39051,7 @@ case "${host_os}" in
      r_ld_library_defaults="/usr/lib64:/lib64:/usr/lib:/lib"
      ;;
    solaris*)
 -    r_ld_library_defaults="/usr/lib:/lib"
 +    r_ld_library_defaults="/usr/lib:/lib:/usr/lib/amd64:/lib/amd64:/usr/lib/64:/lib/64"
      ;;
-   darwin*)
-     r_ld_library_defaults="/usr/X11R6/lib"
+   *)
+     r_ld_library_defaults=
diff --git a/math/R/patches/patch-ad b/math/R/patches/patch-ad
index 9f3ef47665d..f9e7902bb4d 100644
--- a/math/R/patches/patch-ad
+++ b/math/R/patches/patch-ad
@@ -1,7 +1,7 @@
-$NetBSD: patch-ad,v 1.18 2015/05/13 12:48:05 ryoon Exp $
+$NetBSD: patch-ad,v 1.19 2016/04/13 21:04:04 markd Exp $
 Adjust EXTRA_LIBS and @WANT_R_SHLIB_TRUE@R_bin_LDADD
 
---- src/main/Makefile.in.orig	2015-03-18 23:03:54.000000000 +0000
+--- src/main/Makefile.in.orig	2015-12-10 23:15:17.000000000 +0000
 +++ src/main/Makefile.in
 @@ -103,13 +103,13 @@ EXTRA_STATIC_LIBS = \
    $(R_ZLIBS) $(R_BZLIBS) $(R_PCRE) $(R_TRE) $(R_XDR) $(R_XZ) $(R_LIBINTL) $(R_TZONE)
@@ -18,4 +18,4 @@ Adjust EXTRA_LIBS and @WANT_R_SHLIB_TRUE@R_bin_LDADD
 +@WANT_R_SHLIB_TRUE@R_bin_LDADD = -L../../lib@R_ARCH@ ${COMPILER_RPATH_FLAG}$(Rexeclibdir) -lR @BLAS_SHLIB_TRUE@-lRblas
  @BUILD_LTO_FALSE@R_bin_DEPENDENCIES =@WANT_R_SHLIB_FALSE@ libR.a @USE_EXPORTFILES_TRUE@ $(top_builddir)/etc/R.exp
  
- libR_la = libR$(DYLIB_EXT)
+ libR_la = libR$(R_DYLIB_EXT)