Update math/R to 3.0.1-patched, and adjust dependent ports;

synchronize math/rpy with upstream repository

Reviewed by:	wen
Approved by:	wen, tota

1 files changed, 54 insertions, 7 deletions

diff --git a/math/rpy/files/patch-setup.py b/math/rpy/files/patch-setup.py
index 6cc97c1af08f..caeba282d087 100644
--- a/math/rpy/files/patch-setup.py
+++ b/math/rpy/files/patch-setup.py
@@ -1,13 +1,60 @@
---- setup.py.orig	2008-07-29 22:53:21.000000000 +0200
-+++ setup.py	2008-07-29 22:54:04.000000000 +0200
-@@ -159,8 +159,8 @@
-         source_files = source_files + ["src/setenv.c"]
+--- setup.py
++++ setup.py
+@@ -30,13 +30,14 @@ can be used for each of these R versions.
+ See the files INSTALL.UNIX and INSTALL.WINDOWS for more details.
+ """
+ 
+-DEBUG=True
++DEBUG=False
+ 
+ import os, os.path, sys, shutil, re
+ from distutils.core import setup, Extension
+ from distutils.sysconfig import *
+ from distutils.errors import *
+ import rpy_tools
++
+ if sys.platform=="win32":
+     import rpy_wintools
+ 
+@@ -85,7 +86,7 @@ for RHOME in RHOMES:
+         get_config_vars()['OPT'] = '-g -Wall'
+     else:
+         # to avoid strict prototypes errors from R includes
+-        get_config_vars()['OPT'] = '-DNDEBUG -g -O3 -Wall'
++        get_config_vars()['OPT'] = '-DNDEBUG -O3 -Wall'
+ 
+     # get the Python version
+     if sys.version[:3] >= '2.2':
+@@ -149,22 +150,21 @@ for RHOME in RHOMES:
+         library_dirs= r_libs
+         runtime_libs = r_libs
+         extra_compile_args=[]
+-    elif sys.platform=='osf1V5':
+-        include_dirs = [ os.path.join(RHOME.strip(), 'include'), 
+-                         'src' ]
+-        libraries=['R','Rlapack']
+-        library_dirs = r_libs
+-        runtime_libs = r_libs
+-        extra_compile_args=["-shared"]
+-        source_files = source_files + ["src/setenv.c"]
++        
      else: # unix-like systems, this is known to work for Linux and Solaris
          include_dirs = [ os.path.join(RHOME.strip(), 'include'), 
--                         'src', '/usr/share/R/include' ]
+                          'src', '/usr/share/R/include' ]
 -        libraries=['R','Rlapack']
-+                         'src', '%%LOCALBASE%%/lib/R/include' ]
-+        libraries=['R','R']
++
          library_dirs = r_libs
          runtime_libs = r_libs
          extra_compile_args=["-shared"]
+         source_files = source_files + ["src/setenv.c"]
++        
++        libraries=['R']
++          
++        # Ask R to tell us how to properly link against lapack
++        extra_compile_args += [ rpy_tools.get_R_LAPACK_LIB_FLAGS( RHOME ) ]
++
+ 
+     # Discover which array packages are present
+     try: 
+diff --git src/RPy.h src/RPy.h
+index 04faf3d..614ae5a 100644