r: Updates for 3.3.2

conda-archive · Dec 19, 2016 · 5ac9e1c · johanneskoester · May 4, 2017 · mingwandroid
1 parent ce62ca7
commit 5ac9e1c
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Showing 133 changed files with 2,109 additions and 1,245 deletions.
diff --git a/pcre/pcre-8.36.tar.gz b/pcre/pcre-8.36.tar.gz
diff --git a/r-base/0005-Win32-Extend-sqrt-NA_real_-hack-to-all-GCC-versions.patch b/r-base/0005-Win32-Extend-sqrt-NA_real_-hack-to-all-GCC-versions.patch
@@ -1,6 +1,6 @@
 --- src/main/eval.c	2016-01-12 23:15:08.000000000 +0000
 +++ src/main/eval.c.new	2016-04-02 19:37:03.814139700 +0100
-@@ -3753,8 +3753,7 @@
+@@ -3754,8 +3754,7 @@
     called with NA_real_. Not sure this is a bug in the Windows
     toolchain or in our expectations, but these defines attempt to work
     around this. */

diff --git a/r-base/0006-Win32-GCC-5.3-Fix-ISNAN-int-emits-UD2-insn.patch b/r-base/0006-Win32-GCC-5.3-Fix-ISNAN-int-emits-UD2-insn.patch
@@ -1,6 +1,6 @@
 --- src/main/eval.c	2016-04-03 19:46:51.025442100 +0100
 +++ src/main/eval.c.new	2016-04-03 19:46:48.279325900 +0100
-@@ -3754,7 +3754,7 @@
+@@ -3755,7 +3755,7 @@
     toolchain or in our expectations, but these defines attempt to work
     around this. */
  #if (defined(_WIN32) || defined(_WIN64)) && defined(__GNUC__)

diff --git a/r-base/0008-Darwin-set-DYLD_FALLBACK_LIBRARY_PATH.patch b/r-base/0008-Darwin-set-DYLD_FALLBACK_LIBRARY_PATH.patch
@@ -1,6 +1,6 @@
 --- configure.ac.old	2016-06-14 23:07:04.000000000 +0100
 +++ configure.ac	2016-06-14 23:07:11.000000000 +0100
-@@ -673,7 +673,7 @@
+@@ -678,7 +678,7 @@
  R_LD_LIBRARY_PATH_save=${R_LD_LIBRARY_PATH}
  R_LD_LIBRARY_PATH=
  case "${host_os}" in
@@ -11,7 +11,7 @@
      ## This allows the dyld to find libraries even without xx_LIBRARY_PATH.
 --- configure.old	2016-06-14 23:03:38.000000000 +0100
 +++ configure	2016-06-14 23:04:50.000000000 +0100
-@@ -22365,7 +22365,7 @@
+@@ -22373,7 +22373,7 @@
  R_LD_LIBRARY_PATH_save=${R_LD_LIBRARY_PATH}
  R_LD_LIBRARY_PATH=
  case "${host_os}" in

diff --git a/r-base/0009-R-3.3.0-Use-AC_SEARCH_LIBS-to-search-for-ncurses.patch b/r-base/0009-R-3.3.0-Use-AC_SEARCH_LIBS-to-search-for-ncurses.patch
@@ -1,19 +1,18 @@
-From 3dc29158a1c1cd55cbfe1ed0a59192f08a06c5ea Mon Sep 17 00:00:00 2001
+From 75d6348349fd9b3756dca27068b95dfbea31730e Mon Sep 17 00:00:00 2001
 From: Ray Donnelly <[email protected]>
-Date: Tue, 21 Jun 2016 14:31:28 +0100
-Subject: [PATCH 9/9] R-3.3.0: Use AC_SEARCH_LIBS to search for ncurses
+Date: Tue, 21 Jun 2016 14:22:30 +0100
+Subject: [PATCH 9/9] Use AC_SEARCH_LIBS to search for ncursesw then ncurses
 
-First for ncursesw then ncurses.
 ---
  configure    | 62 ++++++++++++++++++++++++++++++++++++++----------------------
  configure.ac |  2 +-
  2 files changed, 40 insertions(+), 24 deletions(-)
 
 diff --git a/configure b/configure
-index e53821d..93d79a5 100755
+index e1abd4b..cfb18c9 100755
 --- a/configure
 +++ b/configure
-@@ -22737,42 +22737,59 @@ fi
+@@ -22745,42 +22745,59 @@
    if test "${use_readline}" = no; then
      ## only need ncurses if libreadline is not statically linked against it
      unset ac_cv_lib_readline_rl_callback_read_char
@@ -93,25 +92,7 @@ index e53821d..93d79a5 100755
 
  else
    { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -ltermcap" >&5
-@@ -25057,7 +25074,7 @@ _ACEOF
- # flags.
- r_save_CFLAGS=$CFLAGS
- CFLAGS="$CFLAGS $r_verb"
--(eval echo $as_me:25060: \"$ac_link\") >&5
-+(eval echo $as_me:25077: \"$ac_link\") >&5
- r_c_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
- echo "$r_c_v_output" >&5
- CFLAGS=$r_save_CFLAGS
-@@ -25132,7 +25149,7 @@ _ACEOF
- # flags.
- r_save_CFLAGS=$CFLAGS
- CFLAGS="$CFLAGS $r_cv_prog_c_v"
--(eval echo $as_me:25135: \"$ac_link\") >&5
-+(eval echo $as_me:25152: \"$ac_link\") >&5
- r_c_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
- echo "$r_c_v_output" >&5
- CFLAGS=$r_save_CFLAGS
-@@ -41663,7 +41680,6 @@ fi
+@@ -41674,7 +41691,6 @@
  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
  $as_echo "$MKDIR_P" >&6; }
 
@@ -120,10 +101,10 @@ index e53821d..93d79a5 100755
  case $mkdir_p in
    [\\/$]* | ?:[\\/]*) ;;
 diff --git a/configure.ac b/configure.ac
-index 9d8be70..6268322 100644
+index 4a28294..52900b7 100644
 --- a/configure.ac
 +++ b/configure.ac
-@@ -764,7 +764,7 @@ if test "${use_readline}" = yes; then
+@@ -769,7 +769,7 @@ if test "${use_readline}" = yes; then
    if test "${use_readline}" = no; then
      ## only need ncurses if libreadline is not statically linked against it
      unset ac_cv_lib_readline_rl_callback_read_char

diff --git a/r-base/0009-Use-AC_SEARCH_LIBS-to-search-for-ncursesw-then-ncurs.patch b/r-base/0009-Use-AC_SEARCH_LIBS-to-search-for-ncursesw-then-ncurs.patch
@@ -12,7 +12,7 @@ diff --git a/configure b/configure
 index e1abd4b..cfb18c9 100755
 --- a/configure
 +++ b/configure
-@@ -22737,42 +22737,59 @@ fi
+@@ -22745,42 +22745,59 @@
    if test "${use_readline}" = no; then
      ## only need ncurses if libreadline is not statically linked against it
      unset ac_cv_lib_readline_rl_callback_read_char
@@ -92,25 +92,7 @@ index e1abd4b..cfb18c9 100755
 
  else
    { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -ltermcap" >&5
-@@ -25063,7 +25080,7 @@ _ACEOF
- # flags.
- r_save_CFLAGS=$CFLAGS
- CFLAGS="$CFLAGS $r_verb"
--(eval echo $as_me:25066: \"$ac_link\") >&5
-+(eval echo $as_me:25083: \"$ac_link\") >&5
- r_c_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
- echo "$r_c_v_output" >&5
- CFLAGS=$r_save_CFLAGS
-@@ -25138,7 +25155,7 @@ _ACEOF
- # flags.
- r_save_CFLAGS=$CFLAGS
- CFLAGS="$CFLAGS $r_cv_prog_c_v"
--(eval echo $as_me:25141: \"$ac_link\") >&5
-+(eval echo $as_me:25158: \"$ac_link\") >&5
- r_c_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
- echo "$r_c_v_output" >&5
- CFLAGS=$r_save_CFLAGS
-@@ -41669,7 +41686,6 @@ fi
+@@ -41674,7 +41691,6 @@
  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5
  $as_echo "$MKDIR_P" >&6; }
 
@@ -122,7 +104,7 @@ diff --git a/configure.ac b/configure.ac
 index 4a28294..52900b7 100644
 --- a/configure.ac
 +++ b/configure.ac
-@@ -764,7 +764,7 @@ if test "${use_readline}" = yes; then
+@@ -769,7 +769,7 @@ if test "${use_readline}" = yes; then
    if test "${use_readline}" = no; then
      ## only need ncurses if libreadline is not statically linked against it
      unset ac_cv_lib_readline_rl_callback_read_char

diff --git a/r-base/0011-Linux-Do-not-modify-LD_LIBRARY_PATH.patch b/r-base/0011-Linux-Do-not-modify-LD_LIBRARY_PATH.patch
@@ -1,6 +1,6 @@
-diff -urN R-3.3.1.old/configure R-3.3.1/configure
---- R-3.3.1.old/configure	2016-10-21 13:04:51.588700987 +0100
-+++ R-3.3.1/configure	2016-10-21 13:09:48.000000000 +0100
+diff -urN R-3.3.2.orig/configure R-3.3.2/configure
+--- R-3.3.2.orig/configure	2016-12-06 14:50:35.000000000 +0000
++++ R-3.3.2/configure	2016-12-06 14:50:35.000000000 +0000
 @@ -777,6 +777,7 @@
  USE_EXPORTFILES_TRUE
  SHLIB_EXT
@@ -9,16 +9,16 @@ diff -urN R-3.3.1.old/configure R-3.3.1/configure
  DYLIB_UNDEFINED_ALLOWED_FALSE
  DYLIB_UNDEFINED_ALLOWED_TRUE
  INTERNET_LIBS
-@@ -22355,7 +22356,7 @@
-
+@@ -22363,7 +22364,7 @@
+ 
  ### * Checks for libraries.
 
 -## Set up LD_LIBRARY_PATH or equivalent.
 +## Add -Wl,-rpath, entries to RPATH_LDFLAGS.
  ## <FIXME>
  ## What is this doing *HERE*?
  ## Should be needed for tests using AC_RUN_IFELSE()?
-@@ -22388,6 +22389,13 @@
+@@ -22396,6 +22397,13 @@
  else
    R_LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}${separator}${lib}"
  fi
@@ -32,7 +32,7 @@ diff -urN R-3.3.1.old/configure R-3.3.1/configure
  	  ;;
        esac
      done
-@@ -22407,13 +22415,20 @@
+@@ -22415,13 +22423,20 @@
      Rshlibpath_var=${shlibpath_var}
  esac
 
@@ -55,45 +55,45 @@ diff -urN R-3.3.1.old/configure R-3.3.1/configure
 
 
  ## record how to strip shared/dynamic libraries.
-@@ -25074,7 +25089,7 @@
+@@ -25082,7 +25097,7 @@
  # flags.
  r_save_CFLAGS=$CFLAGS
  CFLAGS="$CFLAGS $r_verb"
--(eval echo $as_me:25077: \"$ac_link\") >&5
-+(eval echo $as_me:25109: \"$ac_link\") >&5
+-(eval echo $as_me:25068: \"$ac_link\") >&5
++(eval echo $as_me:25117: \"$ac_link\") >&5
  r_c_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
  echo "$r_c_v_output" >&5
  CFLAGS=$r_save_CFLAGS
-@@ -25149,7 +25164,7 @@
+@@ -25157,7 +25172,7 @@
  # flags.
  r_save_CFLAGS=$CFLAGS
  CFLAGS="$CFLAGS $r_cv_prog_c_v"
--(eval echo $as_me:25152: \"$ac_link\") >&5
-+(eval echo $as_me:25184: \"$ac_link\") >&5
+-(eval echo $as_me:25143: \"$ac_link\") >&5
++(eval echo $as_me:25192: \"$ac_link\") >&5
  r_c_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
  echo "$r_c_v_output" >&5
  CFLAGS=$r_save_CFLAGS
-diff -urN R-3.3.1.old/configure.ac R-3.3.1/configure.ac
---- R-3.3.1.old/configure.ac	2016-10-21 13:04:45.171835484 +0100
-+++ R-3.3.1/configure.ac	2016-10-21 13:10:13.000000000 +0100
-@@ -663,7 +663,7 @@
-
+diff -urN R-3.3.2.orig/configure.ac R-3.3.2/configure.ac
+--- R-3.3.2.orig/configure.ac	2016-12-06 14:50:35.000000000 +0000
++++ R-3.3.2/configure.ac	2016-12-06 14:50:35.000000000 +0000
+@@ -668,7 +668,7 @@
+ 
  ### * Checks for libraries.
 
 -## Set up LD_LIBRARY_PATH or equivalent.
 +## Add -Wl,-rpath, entries to RPATH_LDFLAGS.
  ## <FIXME>
  ## What is this doing *HERE*?
  ## Should be needed for tests using AC_RUN_IFELSE()?
-@@ -690,6 +690,7 @@
+@@ -695,6 +695,7 @@
          -L*)
  	  lib=`echo ${arg} | sed "s/^-L//"`
  	  R_SH_VAR_ADD(R_LD_LIBRARY_PATH, [${lib}], [${PATH_SEPARATOR}])
 +          R_SH_VAR_ADD(RPATH_LDFLAGS, [-Wl,-rpath,${lib}])
  	  ;;
        esac
      done
-@@ -709,13 +710,20 @@
+@@ -714,13 +715,20 @@
      Rshlibpath_var=${shlibpath_var}
  esac
  AC_SUBST(shlibpath_var)
@@ -116,17 +116,17 @@ diff -urN R-3.3.1.old/configure.ac R-3.3.1/configure.ac
  AC_SUBST(Rshlibpath_var)
 
  ## record how to strip shared/dynamic libraries.
-@@ -1706,6 +1714,7 @@
-
+@@ -1714,6 +1722,7 @@
+ 
  AC_SUBST(MAIN_LD)
  AC_SUBST(MAIN_LDFLAGS)
 +AC_SUBST(RPATH_LDFLAGS)
  AC_SUBST(CPICFLAGS)
  AC_SUBST(CXXPICFLAGS)
  AC_SUBST(DYLIB_LD)
-diff -urN R-3.3.1.old/etc/ldpaths.in R-3.3.1/etc/ldpaths.in
---- R-3.3.1.old/etc/ldpaths.in	2016-01-09 23:15:11.000000000 +0000
-+++ R-3.3.1/etc/ldpaths.in	2016-10-21 13:05:20.052916181 +0100
+diff -urN R-3.3.2.orig/etc/ldpaths.in R-3.3.2/etc/ldpaths.in
+--- R-3.3.2.orig/etc/ldpaths.in	2016-12-06 14:50:35.000000000 +0000
++++ R-3.3.2/etc/ldpaths.in	2016-12-06 14:50:35.000000000 +0000
 @@ -1,3 +1,17 @@
 +# https://github.com/conda/conda/issues/1679:
 +#  Internally R_system() calls system() which
@@ -145,9 +145,9 @@ diff -urN R-3.3.1.old/etc/ldpaths.in R-3.3.1/etc/ldpaths.in
  : ${JAVA_HOME=@JAVA_HOME@}
  : ${R_JAVA_LD_LIBRARY_PATH=@R_JAVA_LD_LIBRARY_PATH@}
  if test -n "@R_LD_LIBRARY_PATH@"; then
-diff -urN R-3.3.1.old/etc/Makeconf.in R-3.3.1/etc/Makeconf.in
---- R-3.3.1.old/etc/Makeconf.in	2016-03-16 23:04:44.000000000 +0000
-+++ R-3.3.1/etc/Makeconf.in	2016-10-21 13:05:20.052916181 +0100
+diff -urN R-3.3.2.orig/etc/Makeconf.in R-3.3.2/etc/Makeconf.in
+--- R-3.3.2.orig/etc/Makeconf.in	2016-12-06 14:50:35.000000000 +0000
++++ R-3.3.2/etc/Makeconf.in	2016-12-06 14:50:35.000000000 +0000
 @@ -71,7 +71,8 @@
  ## needed to build applications linking to static libR
  MAIN_LD = @MAIN_LD@
@@ -158,9 +158,9 @@ diff -urN R-3.3.1.old/etc/Makeconf.in R-3.3.1/etc/Makeconf.in
  MKINSTALLDIRS = $(R_HOME)/bin/mkinstalldirs
  OBJC = @OBJC@
  OBJCFLAGS = @OBJCFLAGS@ $(LTO)
-diff -urN R-3.3.1.old/Makeconf.in R-3.3.1/Makeconf.in
---- R-3.3.1.old/Makeconf.in	2015-09-08 23:15:15.000000000 +0100
-+++ R-3.3.1/Makeconf.in	2016-10-21 13:05:20.052916181 +0100
+diff -urN R-3.3.2.orig/Makeconf.in R-3.3.2/Makeconf.in
+--- R-3.3.2.orig/Makeconf.in	2016-12-06 14:50:35.000000000 +0000
++++ R-3.3.2/Makeconf.in	2016-12-06 14:50:35.000000000 +0000
 @@ -63,7 +63,8 @@
  MAIN_FFLAGS = @MAIN_FFLAGS@
  MAIN_LD = @MAIN_LD@@BUILD_LTO_TRUE@ $(CFLAGS)

diff --git a/r-base/0012-macOS-include-cairo_h-not-cairo-xlib_h.patch b/r-base/0012-macOS-include-cairo_h-not-cairo-xlib_h.patch
@@ -1,7 +1,7 @@
-diff -urN R-3.3.1.orig/configure R-3.3.1/configure
---- R-3.3.1.orig/configure	2016-11-28 13:26:36.000000000 +0000
-+++ R-3.3.1/configure	2016-11-28 13:30:11.000000000 +0000
-@@ -34399,8 +34399,8 @@
+diff -urN R-3.3.2.orig/configure R-3.3.2/configure
+--- R-3.3.2.orig/configure	2016-12-06 14:52:40.000000000 +0000
++++ R-3.3.2/configure	2016-12-06 14:52:55.000000000 +0000
+@@ -34410,8 +34410,8 @@
         modlist="${modlist} cairo-svg"
         r_cairo_svg=yes
      fi
@@ -12,7 +12,7 @@ diff -urN R-3.3.1.orig/configure R-3.3.1/configure
        else
           xmodlist="${modlist}"
        fi
-@@ -34422,7 +34422,7 @@
+@@ -34433,7 +34433,7 @@
 
  #include <pango/pango.h>
  #include <pango/pangocairo.h>
@@ -21,7 +21,7 @@ diff -urN R-3.3.1.orig/configure R-3.3.1/configure
  #if CAIRO_VERSION  < 10200
  #error cairo version >= 1.2 required
  #endif
-@@ -34486,8 +34486,8 @@
+@@ -34497,8 +34497,8 @@
           modlist="${modlist} cairo-svg"
           r_cairo_svg=yes
        fi
@@ -32,17 +32,17 @@ diff -urN R-3.3.1.orig/configure R-3.3.1/configure
        else
           xmodlist="${modlist}"
        fi
-@@ -34518,7 +34518,6 @@
+@@ -34529,7 +34529,6 @@
  /* end confdefs.h.  */
 
  #include <cairo.h>
 -#include <cairo-xlib.h>
  #if CAIRO_VERSION  < 10200
  #error cairo version >= 1.2 required
  #endif
-diff -urN R-3.3.1.orig/m4/cairo.m4 R-3.3.1/m4/cairo.m4
---- R-3.3.1.orig/m4/cairo.m4	2016-11-28 13:26:36.000000000 +0000
-+++ R-3.3.1/m4/cairo.m4	2016-11-28 13:29:36.000000000 +0000
+diff -urN R-3.3.2.orig/m4/cairo.m4 R-3.3.2/m4/cairo.m4
+--- R-3.3.2.orig/m4/cairo.m4	2016-12-06 14:50:35.000000000 +0000
++++ R-3.3.2/m4/cairo.m4	2016-12-06 14:52:55.000000000 +0000
 @@ -52,8 +52,8 @@
         modlist="${modlist} cairo-svg"
         r_cairo_svg=yes

diff --git a/r-base/meta.yaml b/r-base/meta.yaml
@@ -1,14 +1,14 @@
 {% set native = 'm2w64-' if win else '' %}
 {% set posix= 'm24-' if win else '' %}
-{% set ver= '3.3.1' %}
+{% set ver= '3.3.2' %}
 
 package:
   name: r-base
   version: {{ ver }}
 
 source:
   url: https://cran.r-project.org/src/base/R-3/R-{{ ver }}.tar.gz
-  sha1: df853188d3e2b1c2d32393016401c432a5192c4d
+  sha1: 0e39e9c2d28fe6bab9c55ca23e08ba8727fd2fca
   patches:
     - mac-unicode.patch # [osx]
     - 0002-Win32-Fix-trio-config-h-include-depth-issue.patch
@@ -19,12 +19,10 @@ source:
     - 0007-Win32-MSYS2-ENV_CONV_EXCL_R_ARCH.patch
     - 0008-Darwin-set-DYLD_FALLBACK_LIBRARY_PATH.patch
     - 0009-R-3.3.0-Use-AC_SEARCH_LIBS-to-search-for-ncurses.patch
-    - 0010-configure-Fix-typo-CPPLAGS.patch
     - 0011-Linux-Do-not-modify-LD_LIBRARY_PATH.patch
     - 0012-macOS-include-cairo_h-not-cairo-xlib_h.patch
 
 build:
-  number: 6
   rpaths:
     - lib/R/lib/
     - lib/
@@ -62,6 +60,7 @@ requirements:
     - {{native}}icu            # [win]
     - {{native}}pcre 8.39*     # [not win]
     - {{native}}pcre           # [win]
+    - mkl
     - {{native}}tk
     - {{native}}zlib
     - {{native}}gsl
@@ -94,6 +93,7 @@ requirements:
     - {{native}}icu            # [win]
     - {{native}}pcre 8.39*     # [not win]
     - {{native}}pcre           # [win]
+    - mkl
     - {{native}}tk
     - {{native}}zlib
     - {{native}}gsl