math/R: 3.2.2 -> 3.3.0

Changes: https://stat.ethz.ch/pipermail/r-announce/2016/000602.html

PR:		209315
Submitted by:	wen
Approved by:	bf (maintainer, by mail)

6 files changed, 44 insertions, 38 deletions

diff --git a/math/R/Makefile b/math/R/Makefile
index 1d5cdcb07477..9bba13b53bd1 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME?=	R
-PORTVERSION=	3.2.2
-PORTREVISION=	1
+PORTVERSION=	3.3.0
 CATEGORIES=	math lang
 MASTER_SITES=	http://cran.r-project.org/%SUBDIR%/ \
 		ftp://cran.r-project.org/pub/R/%SUBDIR%/ \
@@ -29,6 +28,7 @@ LICENSE=	GPLv2
 
 BUILD_DEPENDS=		${LOCALBASE}/bin/gsed:textproc/gsed \
 			texi2dvi:print/texinfo
+LIB_DEPENDS=		libcurl.so:ftp/curl
 
 CONFIGURE_ENV=		LIBR_LDFLAGS="${LDFLAGS}" OBJC="${CC}" \
 			SED="${LOCALBASE}/bin/gsed" \
diff --git a/math/R/distinfo b/math/R/distinfo
index 49560340f657..14d04e689f13 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,2 +1,2 @@
-SHA256 (R-3.2.2.tar.gz) = 9c9152e74134b68b0f3a1c7083764adc1cb56fd8336bec003fd0ca550cd2461d
-SIZE (R-3.2.2.tar.gz) = 29772864
+SHA256 (R-3.3.0.tar.gz) = 9256b154b1a5993d844bee7b1955cd49c99ad72cef03cce3cd1bdca1310311e4
+SIZE (R-3.3.0.tar.gz) = 29820067
diff --git a/math/R/files/patch-configure b/math/R/files/patch-configure
index 238406c79108..da96c4789130 100644
--- a/math/R/files/patch-configure
+++ b/math/R/files/patch-configure
@@ -1,81 +1,81 @@
---- configure.orig	2015-08-13 09:21:16 UTC
+--- configure.orig	2016-04-25 22:17:08 UTC
 +++ configure
-@@ -20589,13 +20589,13 @@ if test "x$ac_cv_lib_mw__mwvalidcheckl" 
-   LIBM="-lmw"
+@@ -22470,13 +22470,13 @@ if test "x$ac_cv_lib_mw__mwvalidcheckl" 
+   LIBM=-lmw
  fi
  
 -  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lm" >&5
 -$as_echo_n "checking for cos in -lm... " >&6; }
-+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lquadmath -lm" >&5
-+$as_echo_n "checking for cos in -lquadmath -lm... " >&6; }
++  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lquadmath -lquadmath -lm" >&5
++$as_echo_n "checking for cos in -lquadmath -lquadmath -lm... " >&6; }
  if ${ac_cv_lib_m_cos+:} false; then :
    $as_echo_n "(cached) " >&6
  else
    ac_check_lib_save_LIBS=$LIBS
 -LIBS="-lm  $LIBS"
-+LIBS="-lquadmath -lm  $LIBS"
++LIBS="-lquadmath -lquadmath -lm  $LIBS"
  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
  /* end confdefs.h.  */
  
-@@ -20626,18 +20626,18 @@ fi
+@@ -22507,18 +22507,18 @@ fi
  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_cos" >&5
  $as_echo "$ac_cv_lib_m_cos" >&6; }
  if test "x$ac_cv_lib_m_cos" = xyes; then :
 -  LIBM="$LIBM -lm"
-+  LIBM="$LIBM -lquadmath -lm"
++  LIBM="$LIBM -lquadmath -lquadmath -lm"
  fi
  
    ;;
  *)
 -  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lm" >&5
 -$as_echo_n "checking for cos in -lm... " >&6; }
-+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lquadmath -lm" >&5
-+$as_echo_n "checking for cos in -lquadmath -lm... " >&6; }
++  { $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lquadmath -lquadmath -lm" >&5
++$as_echo_n "checking for cos in -lquadmath  -lquadmath -lm... " >&6; }
  if ${ac_cv_lib_m_cos+:} false; then :
    $as_echo_n "(cached) " >&6
  else
    ac_check_lib_save_LIBS=$LIBS
 -LIBS="-lm  $LIBS"
-+LIBS="-lquadmath -lm  $LIBS"
++LIBS="-lquadmath -lquadmath -lm  $LIBS"
  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
  /* end confdefs.h.  */
  
-@@ -20668,7 +20668,7 @@ fi
+@@ -22549,7 +22549,7 @@ fi
  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_cos" >&5
  $as_echo "$ac_cv_lib_m_cos" >&6; }
  if test "x$ac_cv_lib_m_cos" = xyes; then :
--  LIBM="-lm"
-+  LIBM="-lquadmath -lm"
+-  LIBM=-lm
++  LIBM="-lquadmath -lquadmath -lm"
  fi
  
    ;;
-@@ -20679,13 +20679,13 @@ esac
+@@ -22560,13 +22560,13 @@ esac
  ## </NOTE>
  ## AC_CHECK_LIBM computes LIBM but does not add to LIBS, hence we do
  ## the following as well.
 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for sin in -lm" >&5
 -$as_echo_n "checking for sin in -lm... " >&6; }
-+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for sin in -lquadmath -lm" >&5
-+$as_echo_n "checking for sin in -lquadmath -lm... " >&6; }
++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for sin in -lquadmath -lquadmath -lm" >&5
++$as_echo_n "checking for sin in -lquadmath -lquadmath -lm... " >&6; }
  if ${ac_cv_lib_m_sin+:} false; then :
    $as_echo_n "(cached) " >&6
  else
    ac_check_lib_save_LIBS=$LIBS
 -LIBS="-lm  $LIBS"
-+LIBS="-lquadmath -lm  $LIBS"
++LIBS="-lquadmath -lquadmath -lm  $LIBS"
  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
  /* end confdefs.h.  */
  
-@@ -20720,7 +20720,7 @@ if test "x$ac_cv_lib_m_sin" = xyes; then
+@@ -22601,7 +22601,7 @@ if test "x$ac_cv_lib_m_sin" = xyes; then
  #define HAVE_LIBM 1
  _ACEOF
  
 -  LIBS="-lm $LIBS"
-+  LIBS="-lquadmath -lm $LIBS"
++  LIBS="-lquadmath -lquadmath -lm $LIBS"
  
  fi
  
-@@ -26166,7 +26166,7 @@ fi
+@@ -27958,7 +27958,7 @@ fi
  ## if nothing was obtained for SHLIB_CXXLDFLAGS.
  ##
  ## Note also that some systems (formerly AIX) do not allow for unresolved
@@ -84,16 +84,16 @@
  ## it exists) when building a shlib module via SHLIB_LIBADD.
  
  main_ld="${CC}"
-@@ -28310,7 +28310,7 @@ if ${ac_cv_lib_rt_clock_gettime+:} false
+@@ -30147,7 +30147,7 @@ if ${ac_cv_lib_rt_clock_gettime+:} false
    $as_echo_n "(cached) " >&6
  else
    ac_check_lib_save_LIBS=$LIBS
 -LIBS="-lrt  $LIBS"
-+LIBS=" $LIBS"
++LIBS="$LIBS"
  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
  /* end confdefs.h.  */
  
-@@ -28353,7 +28353,7 @@ if test "x$ac_cv_lib_rt_clock_gettime" =
+@@ -30190,7 +30190,7 @@ if test "x$ac_cv_lib_rt_clock_gettime" =
  #define HAVE_LIBRT 1
  _ACEOF
  
@@ -102,7 +102,7 @@
  
  fi
  
-@@ -33267,7 +33267,7 @@ fi
+@@ -35109,7 +35109,7 @@ fi
      ## Part 2.  Try finding the tk library.
      if test -n "${TK_CONFIG}"; then
        . ${TK_CONFIG}
diff --git a/math/R/files/patch-src__nmath__standalone__test.c b/math/R/files/patch-src__nmath__standalone__test.c
index 582d1cb24594..0aefc4bf9fc6 100644
--- a/math/R/files/patch-src__nmath__standalone__test.c
+++ b/math/R/files/patch-src__nmath__standalone__test.c
@@ -1,4 +1,4 @@
---- src/nmath/standalone/test.c.orig	2012-04-15 22:05:35 UTC
+--- src/nmath/standalone/test.c.orig	2015-08-25 22:18:53 UTC
 +++ src/nmath/standalone/test.c
 @@ -38,7 +38,7 @@ main(int argc, char** argv)
      qnorm(0.7, 0.0, 1.0, 0, 0);
diff --git a/math/R/files/patch-src_extra_tre_tre-internal.h b/math/R/files/patch-src_extra_tre_tre-internal.h
index 36a8c997fe16..9648c7b240ce 100644
--- a/math/R/files/patch-src_extra_tre_tre-internal.h
+++ b/math/R/files/patch-src_extra_tre_tre-internal.h
@@ -1,4 +1,4 @@
---- src/extra/tre/tre-internal.h.orig	2014-06-13 22:15:07 UTC
+--- src/extra/tre/tre-internal.h.orig	2016-05-05 10:54:54 UTC
 +++ src/extra/tre/tre-internal.h
 @@ -17,6 +17,7 @@
  #include <wctype.h>
@@ -8,15 +8,15 @@
  #include <ctype.h>
  #include "tre.h"
  
-@@ -48,7 +49,11 @@
+@@ -47,7 +48,11 @@
+ #ifdef TRE_WCHAR
  
  /* Wide characters. */
- typedef wint_t tre_cint_t;
 +#if WCHAR_MAX <= INT_MAX
- #define TRE_CHAR_MAX WCHAR_MAX
+ typedef wint_t tre_cint_t;
 +#else /* WCHAR_MAX > INT_MAX */
 +#define TRE_CHAR_MAX INT_MAX
 +#endif
- 
- #ifdef TRE_MULTIBYTE
- #define TRE_MB_CUR_MAX MB_CUR_MAX
+ /* Workaround problem seen on AIX, (2010 & 2015), e.g.,
+     https://stat.ethz.ch/pipermail/r-devel/2015-October/071902.html
+   WCHAR_MAX = UINT32_MAX on AIX and that is "not possible to work"
diff --git a/math/R/pkg-plist b/math/R/pkg-plist
index 9b6f3c645871..bb7297e2ed8d 100644
--- a/math/R/pkg-plist
+++ b/math/R/pkg-plist
@@ -17,7 +17,6 @@
 %%DOCSDIR%%/html/index.html
 %%DOCSDIR%%/html/left.jpg
 %%DOCSDIR%%/html/logo.jpg
-%%DOCSDIR%%/html/logosm.jpg
 %%DOCSDIR%%/html/packages-head-utf8.html
 %%DOCSDIR%%/html/packages.html
 %%DOCSDIR%%/html/resources.html
@@ -180,6 +179,7 @@ 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/NEWS.Rd
 lib/R/library/Matrix/Meta/Rd.rds
 lib/R/library/Matrix/Meta/data.rds
@@ -1059,6 +1059,8 @@ lib/R/library/survival/doc/timedep.R
 lib/R/library/survival/doc/timedep.Rnw
 lib/R/library/survival/doc/timedep.pdf
 lib/R/library/survival/doc/validate.pdf
+lib/R/library/survival/doc/validate.R
+lib/R/library/survival/doc/validate.Rnw
 lib/R/library/survival/help/AnIndex
 lib/R/library/survival/help/aliases.rds
 lib/R/library/survival/help/paths.rds
@@ -1413,6 +1415,8 @@ lib/R/library/utils/Meta/nsInfo.rds
 lib/R/library/utils/Meta/package.rds
 %%PORTDOCS%%%%PDF_MANUAL%%lib/R/library/utils/Meta/vignette.rds
 lib/R/library/utils/NAMESPACE
+lib/R/library/utils/R/sysdata.rdb
+lib/R/library/utils/R/sysdata.rdx
 lib/R/library/utils/R/utils
 lib/R/library/utils/R/utils.rdb
 lib/R/library/utils/R/utils.rdx
@@ -1484,6 +1488,8 @@ lib/R/share/texmf/tex/latex/ts1aett.fd
 man/man1/R.1.gz
 man/man1/Rscript.1.gz
 %%DOCSDIR%%/html/NEWS.2.html
+%%PORTDOCS%%%%DOCSDIR%%/html/Rlogo.pdf
+%%PORTDOCS%%%%DOCSDIR%%/html/Rlogo.svg
 %%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-FAQ.pdf
 %%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-admin.pdf
 %%PORTDOCS%%%%PDF_MANUAL%%%%DOCSDIR%%/manual/R-data.pdf