--- /dev/null
+--- rpy-1.0.2.orig/examples/faithful.dat 1970-01-01 01:00:00.000000000 +0100
++++ rpy-1.0.2/examples/faithful.dat 2010-04-15 17:44:06.000000000 +0100
+@@ -0,0 +1,273 @@
++"eruptions" "waiting"
++3.6 79
++1.8 54
++3.333 74
++2.283 62
++4.533 85
++2.883 55
++4.7 88
++3.6 85
++1.95 51
++4.35 85
++1.833 54
++3.917 84
++4.2 78
++1.75 47
++4.7 83
++2.167 52
++1.75 62
++4.8 84
++1.6 52
++4.25 79
++1.8 51
++1.75 47
++3.45 78
++3.067 69
++4.533 74
++3.6 83
++1.967 55
++4.083 76
++3.85 78
++4.433 79
++4.3 73
++4.467 77
++3.367 66
++4.033 80
++3.833 74
++2.017 52
++1.867 48
++4.833 80
++1.833 59
++4.783 90
++4.35 80
++1.883 58
++4.567 84
++1.75 58
++4.533 73
++3.317 83
++3.833 64
++2.1 53
++4.633 82
++2 59
++4.8 75
++4.716 90
++1.833 54
++4.833 80
++1.733 54
++4.883 83
++3.717 71
++1.667 64
++4.567 77
++4.317 81
++2.233 59
++4.5 84
++1.75 48
++4.8 82
++1.817 60
++4.4 92
++4.167 78
++4.7 78
++2.067 65
++4.7 73
++4.033 82
++1.967 56
++4.5 79
++4 71
++1.983 62
++5.067 76
++2.017 60
++4.567 78
++3.883 76
++3.6 83
++4.133 75
++4.333 82
++4.1 70
++2.633 65
++4.067 73
++4.933 88
++3.95 76
++4.517 80
++2.167 48
++4 86
++2.2 60
++4.333 90
++1.867 50
++4.817 78
++1.833 63
++4.3 72
++4.667 84
++3.75 75
++1.867 51
++4.9 82
++2.483 62
++4.367 88
++2.1 49
++4.5 83
++4.05 81
++1.867 47
++4.7 84
++1.783 52
++4.85 86
++3.683 81
++4.733 75
++2.3 59
++4.9 89
++4.417 79
++1.7 59
++4.633 81
++2.317 50
++4.6 85
++1.817 59
++4.417 87
++2.617 53
++4.067 69
++4.25 77
++1.967 56
++4.6 88
++3.767 81
++1.917 45
++4.5 82
++2.267 55
++4.65 90
++1.867 45
++4.167 83
++2.8 56
++4.333 89
++1.833 46
++4.383 82
++1.883 51
++4.933 86
++2.033 53
++3.733 79
++4.233 81
++2.233 60
++4.533 82
++4.817 77
++4.333 76
++1.983 59
++4.633 80
++2.017 49
++5.1 96
++1.8 53
++5.033 77
++4 77
++2.4 65
++4.6 81
++3.567 71
++4 70
++4.5 81
++4.083 93
++1.8 53
++3.967 89
++2.2 45
++4.15 86
++2 58
++3.833 78
++3.5 66
++4.583 76
++2.367 63
++5 88
++1.933 52
++4.617 93
++1.917 49
++2.083 57
++4.583 77
++3.333 68
++4.167 81
++4.333 81
++4.5 73
++2.417 50
++4 85
++4.167 74
++1.883 55
++4.583 77
++4.25 83
++3.767 83
++2.033 51
++4.433 78
++4.083 84
++1.833 46
++4.417 83
++2.183 55
++4.8 81
++1.833 57
++4.8 76
++4.1 84
++3.966 77
++4.233 81
++3.5 87
++4.366 77
++2.25 51
++4.667 78
++2.1 60
++4.35 82
++4.133 91
++1.867 53
++4.6 78
++1.783 46
++4.367 77
++3.85 84
++1.933 49
++4.5 83
++2.383 71
++4.7 80
++1.867 49
++3.833 75
++3.417 64
++4.233 76
++2.4 53
++4.8 94
++2 55
++4.15 76
++1.867 50
++4.267 82
++1.75 54
++4.483 75
++4 78
++4.117 79
++4.083 78
++4.267 78
++3.917 70
++4.55 79
++4.083 70
++2.417 54
++4.183 86
++2.217 50
++4.45 90
++1.883 54
++1.85 54
++4.283 77
++3.95 79
++2.333 64
++4.15 75
++2.35 47
++4.933 86
++2.9 63
++4.583 85
++3.833 82
++2.083 57
++4.367 82
++2.133 67
++4.35 74
++2.2 54
++4.45 83
++3.567 73
++4.5 73
++4.15 88
++3.817 80
++3.917 71
++4.45 83
++2 56
++4.283 79
++4.767 78
++4.533 84
++1.85 58
++4.25 83
++1.983 43
++2.25 60
++4.75 75
++4.117 81
++2.15 46
++4.417 90
++1.817 46
++4.467 74
+--- rpy-1.0.2.orig/examples/nnet.py 1970-01-01 01:00:00.000000000 +0100
++++ rpy-1.0.4/examples/nnet.py 2010-04-15 17:44:06.000000000 +0100
+@@ -0,0 +1,29 @@
++from rpy import *
++
++# avoid automatic conversion
++set_default_mode(NO_CONVERSION)
++
++
++r.library("nnet")
++model = r("Fxy~x+y")
++
++df = r.data_frame(x = r.c(0,2,5,10,15)
++ ,y = r.c(0,2,5,8,10)
++ ,Fxy = r.c(0,2,5,8,10))
++
++NNModel = r.nnet(model, data = df
++ , size =10, decay =1e-3
++ , lineout=True, skip=True
++ , maxit=1000, Hess =True)
++
++XG = r.expand_grid(x = r.seq(0,7,1), y = r.seq(0,7,1))
++x = r.seq(0,7,1)
++y = r.seq(0,7,1)
++
++
++# turn automatic conversion back on
++set_default_mode(BASIC_CONVERSION)
++
++fit = r.predict(NNModel,XG)
++print fit
++
+--- rpy-1.0.2/PKG-INFO 2008-04-10 17:54:36.000000000 +0100
++++ rpy-1.0.4.orig/PKG-INFO 1970-01-01 01:00:00.000000000 +0100
+@@ -1,13 +0,0 @@
+-Metadata-Version: 1.0
+-Name: rpy
+-Version: 1.0.2
+-Summary: Python interface to the R language
+-Home-page: http://rpy.sourceforge.net
+-Author: Gregory R. Warnes
+-Author-email: warnes@bst.rochester.edu
+-License: GPL
+-Description: RPy provides a robust Python interface to the R
+- programming language. It can manage all kinds of R objects and can
+- execute arbitrary R functions. All the errors from the R language are
+- converted to Python exceptions.
+-Platform: UNKNOWN
+--- rpy-1.0.2.orig/rpy.py 2008-01-02 17:57:09.000000000 +0000
++++ rpy-1.0.2/rpy.py 2010-04-15 17:44:06.000000000 +0100
+@@ -16,7 +16,7 @@
+ #
+ # High level module for managing the lookup of R objects.
+ #
+-# $Id: rpy-1.0.2-R210.patch,v 1.1 2010/04/15 21:58:10 bicatali Exp $
++# $Id: rpy-1.0.2-R210.patch,v 1.1 2010/04/15 21:58:10 bicatali Exp $
+ #
+ #
+ from __future__ import nested_scopes
+@@ -139,6 +139,7 @@
+
+ # Version
+ from rpy_version import rpy_version
++__version__ = rpy_version
+
+ # Symbolic names for conversion modes
+ TOP_CONVERSION = 4
+@@ -332,7 +333,7 @@
+ self.print_(helpobj)
+
+ def __repr__(self):
+- Rver = self.__getitem__('R_version_string')
++ Rver = self.__getitem__('R.version.string')
+ return "RPy version %s [%s]" % (rpy_version, Rver)
+
+ def __str__(self):
+--- rpy-1.0.2.orig/rpy_tools.py 2010-04-15 17:53:14.000000000 +0100
++++ rpy-1.0.2/rpy_tools.py 2010-04-15 17:44:06.000000000 +0100
+@@ -97,8 +97,7 @@
+ if stat or len(output)<=0:
+ raise RuntimeError("Couldn't execute the R interpreter" +
+ " `%s'.\n" % rexec )
+- # edd 05 Apr 2006 version = re.search("R +([0-9]\.[0-9]\.[0-9])", output)
+- version = re.search(" version ([0-9]\.[0-9]\.[0-9])", output)
++ version = re.search(" +([0-9]+\.[0-9]+\.[0-9]+)", output)
+ if not version:
+ raise RuntimeError("Couldn't obtain version number from output\n"
+ "of `R --version'.\n")
+@@ -143,3 +142,20 @@
+ % PYTHON_DIR )
+
+ return PYTHON_DIR
++
++def get_R_LAPACK_LIB_FLAGS(RHOME=get_R_HOME()):
++ """
++ Determine the necessary link arguments for lapack
++ """
++ rexec = os.path.join(RHOME, 'bin', 'R')
++ stat, output = getstatusoutput('"%s" CMD config LAPACK_LIBS' % rexec )
++ if stat or len(output)<=0:
++ raise RuntimeError("Couldn't execute the R interpreter" +
++ " `%s'.\n" % rexec )
++
++ LAPACK_LIB_FLAGS = output.strip()
++ if not LAPACK_LIB_FLAGS:
++ raise RuntimeError("Couldn't obtain LAPACK_LIBS information from output\n"
++ "of `R CMD config LAPACK_LIBS'.\n")
++
++ return LAPACK_LIB_FLAGS
+--- rpy-1.0.2.orig/rpy_version.py 2008-04-03 14:51:23.000000000 +0100
++++ rpy-1.0.2/rpy_version.py 2010-04-15 17:44:06.000000000 +0100
+@@ -1 +1 @@
+-rpy_version = "1.0.2"
++rpy_version = "1.0.3"
+--- rpy-1.0.2.orig/setup.py 2007-11-27 02:06:32.000000000 +0000
++++ rpy-1.0.2/setup.py 2010-04-15 17:44:06.000000000 +0100
+@@ -30,13 +30,14 @@
+ See the files INSTALL.UNIX and INSTALL.WINDOWS for more details.
+ """
+
+-DEBUG=True
++DEBUG=False
+
+-import os, os.path, sys, shutil
++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
+
+@@ -66,6 +67,15 @@
+ #if sys.platform=="win32":
+ # rpy_wintools.CreatePythonWinLib()
+
++# On Mac OS X ("darwin") it is necessary to change the symlink
++# /Library/Frameworks/R.framework/Versions/Current
++# to point to the current version of R in
++# /Library/Frameworks/R.framework/Versions/X.Y
++# for that version of R to execute. So, we need to store the original
++# symlink here so we can restore it when we are done
++if sys.platform=="darwin":
++ darwin_original_version = os.readlink("/Library/Frameworks/R.framework/Versions/Current")
++
+ modules = []
+ for RHOME in RHOMES:
+
+@@ -76,7 +86,7 @@
+ 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':
+@@ -87,6 +97,16 @@
+ UNDEF = []
+
+ # configure the R paths
++ #if sys.platform=="darwin":
++ # version =
++ # if os.symlink("/Library/Frameworks/R.framework/Versions/Current")
++ # if RHOME.endswith('/'):
++ # RHOME = RHOME[:-1]
++ # print "RHOME=",os.path.join(os.path.dirname(RHOME),
++ # os.readlink(RHOME) )
++ # sys.exit()
++
++
+ RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
+ RVER = rpy_tools.get_R_VERSION_CODE(RVERSION)
+
+@@ -130,22 +150,21 @@
+ 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' ]
+- libraries=['R','Rlapack']
++
+ 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:
+--- rpy-1.0.2.orig/src/io.c 2008-01-02 17:34:22.000000000 +0000
++++ rpy-1.0.2/src/io.c 2010-04-15 17:44:06.000000000 +0100
+@@ -130,7 +130,7 @@
+ PyErr_Clear();
+ return 0;
+ }
+- snprintf(buf, len, "%s", PyString_AsString(input_data));
++ snprintf( (char*) buf, len, "%s", PyString_AsString(input_data));
+ Py_DECREF(input_data);
+ return 1;
+ }
+--- rpy-1.0.2.orig/src/RPy.h 2010-04-15 17:52:52.000000000 +0100
++++ rpy-1.0.4/src/RPy.h 2010-04-15 17:44:06.000000000 +0100
+@@ -52,6 +52,13 @@
+ #include <Rdefines.h>
+ #include <Rinternals.h>
+ #include <Rversion.h>
++
++#if (R_VERSION >= R_Version(2,4,0))
++#include <Rembedded.h>
++#endif
++
++
++
+ #undef _POSIX_C_SOURCE
+ #include <Python.h>
+ #include <R_ext/Rdynload.h>
+@@ -74,9 +81,8 @@
+ # endif
+ #endif /* _WIN32 */
+
+-#if R_VERSION < 133120
+-#include <Rdevices.h> /* must follow Graphics.h */
+-#endif
++#include <Rembedded.h> /* must follow Graphics.h */
++
+
+ /* Missing definitions from Rinterface.h or RStartup.h */
+ # define CleanEd Rf_CleanEd
+--- rpy-1.0.2.orig/src/rpymodule.c 2010-04-15 17:52:33.000000000 +0100
++++ rpy-1.0.4/src/rpymodule.c 2010-04-15 17:44:06.000000000 +0100
+@@ -1772,13 +1772,15 @@
+
+ void r_finalize(void)
+ {
++#if (R_VERSION < R_Version(2,4,0))
+ unsigned char buf[1024];
+ char * tmpdir;
++#endif
+
+ R_dot_Last();
+ R_RunExitFinalizers();
+ CleanEd();
+-#if (R_VERSION >= R_Version(2,7,0))
++#if (R_VERSION >= R_Version(2,7,0))
+ Rf_KillAllDevices();
+ #else
+ KillAllDevices();
projects / gentoo.git / commitdiff