Update py-rpy to 2.1.3

Works with recent R and recent python.

4 files changed, 179 insertions, 45 deletions

diff --git a/math/py-rpy/Makefile b/math/py-rpy/Makefile
index e6699fbfbed..10e15dd61bb 100644
--- a/math/py-rpy/Makefile
+++ b/math/py-rpy/Makefile
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.25 2010/02/15 16:32:20 joerg Exp $
+# $NetBSD: Makefile,v 1.26 2010/06/09 21:04:26 markd Exp $
 #
 
-DISTNAME=	rpy-0.99.0
-PKGREVISION=	3
-PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
+DISTNAME=	rpy2-2.1.3
+PKGNAME=	${PYPKGPREFIX}-rpy-2.1.3
 CATEGORIES=	math python
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=rpy/}
 
@@ -14,12 +13,11 @@ COMMENT=	R interface for Python
 PKG_DESTDIR_SUPPORT=	user-destdir
 
 PYDISTUTILSPKG=		YES
+USE_LANGUAGES+=		c fortran
 
-BUILDLINK_API_DEPENDS.R+= R>=2.7.0
-
-BROKEN=		Doesn't support modern R.
+BUILDLINK_API_DEPENDS.R+= R>=2.11.0
 
 .include "../../lang/python/extension.mk"
-.include "../../math/py-Numeric/buildlink3.mk"
+.include "../../math/py-numpy/buildlink3.mk"
 .include "../../math/R/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/math/py-rpy/PLIST b/math/py-rpy/PLIST
index 4d829d5439c..91eb097450f 100644
--- a/math/py-rpy/PLIST
+++ b/math/py-rpy/PLIST
@@ -1,20 +1,136 @@
-@comment $NetBSD: PLIST,v 1.11 2008/09/19 14:39:00 joerg Exp $
-${PYSITELIB}/_rpy2072.so
-${PYSITELIB}/rpy.py
-${PYSITELIB}/rpy.pyc
-${PYSITELIB}/rpy.pyo
-${PYSITELIB}/rpy_io.py
-${PYSITELIB}/rpy_io.pyc
-${PYSITELIB}/rpy_io.pyo
-${PYSITELIB}/rpy_options.py
-${PYSITELIB}/rpy_options.pyc
-${PYSITELIB}/rpy_options.pyo
-${PYSITELIB}/rpy_tools.py
-${PYSITELIB}/rpy_tools.pyc
-${PYSITELIB}/rpy_tools.pyo
-${PYSITELIB}/rpy_version.py
-${PYSITELIB}/rpy_version.pyc
-${PYSITELIB}/rpy_version.pyo
-${PYSITELIB}/rpy_wintools.py
-${PYSITELIB}/rpy_wintools.pyc
-${PYSITELIB}/rpy_wintools.pyo
+@comment $NetBSD: PLIST,v 1.12 2010/06/09 21:04:26 markd Exp $
+${PYSITELIB}/rpy2/__init__.py
+${PYSITELIB}/rpy2/__init__.pyc
+${PYSITELIB}/rpy2/__init__.pyo
+${PYSITELIB}/rpy2/images/rpy2_logo.png
+${PYSITELIB}/rpy2/rinterface/__init__.py
+${PYSITELIB}/rpy2/rinterface/__init__.pyc
+${PYSITELIB}/rpy2/rinterface/__init__.pyo
+${PYSITELIB}/rpy2/rinterface/rinterface.so
+${PYSITELIB}/rpy2/rinterface/rpy_device.so
+${PYSITELIB}/rpy2/rinterface/tests/__init__.py
+${PYSITELIB}/rpy2/rinterface/tests/__init__.pyc
+${PYSITELIB}/rpy2/rinterface/tests/__init__.pyo
+${PYSITELIB}/rpy2/rinterface/tests/test_Device.py
+${PYSITELIB}/rpy2/rinterface/tests/test_Device.pyc
+${PYSITELIB}/rpy2/rinterface/tests/test_Device.pyo
+${PYSITELIB}/rpy2/rinterface/tests/test_EmbeddedR.py
+${PYSITELIB}/rpy2/rinterface/tests/test_EmbeddedR.pyc
+${PYSITELIB}/rpy2/rinterface/tests/test_EmbeddedR.pyo
+${PYSITELIB}/rpy2/rinterface/tests/test_Sexp.py
+${PYSITELIB}/rpy2/rinterface/tests/test_Sexp.pyc
+${PYSITELIB}/rpy2/rinterface/tests/test_Sexp.pyo
+${PYSITELIB}/rpy2/rinterface/tests/test_SexpClosure.py
+${PYSITELIB}/rpy2/rinterface/tests/test_SexpClosure.pyc
+${PYSITELIB}/rpy2/rinterface/tests/test_SexpClosure.pyo
+${PYSITELIB}/rpy2/rinterface/tests/test_SexpEnvironment.py
+${PYSITELIB}/rpy2/rinterface/tests/test_SexpEnvironment.pyc
+${PYSITELIB}/rpy2/rinterface/tests/test_SexpEnvironment.pyo
+${PYSITELIB}/rpy2/rinterface/tests/test_SexpVector.py
+${PYSITELIB}/rpy2/rinterface/tests/test_SexpVector.pyc
+${PYSITELIB}/rpy2/rinterface/tests/test_SexpVector.pyo
+${PYSITELIB}/rpy2/rinterface/tests/test_SexpVectorNumeric.py
+${PYSITELIB}/rpy2/rinterface/tests/test_SexpVectorNumeric.pyc
+${PYSITELIB}/rpy2/rinterface/tests/test_SexpVectorNumeric.pyo
+${PYSITELIB}/rpy2/rlike/__init__.py
+${PYSITELIB}/rpy2/rlike/__init__.pyc
+${PYSITELIB}/rpy2/rlike/__init__.pyo
+${PYSITELIB}/rpy2/rlike/container.py
+${PYSITELIB}/rpy2/rlike/container.pyc
+${PYSITELIB}/rpy2/rlike/container.pyo
+${PYSITELIB}/rpy2/rlike/functional.py
+${PYSITELIB}/rpy2/rlike/functional.pyc
+${PYSITELIB}/rpy2/rlike/functional.pyo
+${PYSITELIB}/rpy2/rlike/indexing.py
+${PYSITELIB}/rpy2/rlike/indexing.pyc
+${PYSITELIB}/rpy2/rlike/indexing.pyo
+${PYSITELIB}/rpy2/rlike/tests/__init__.py
+${PYSITELIB}/rpy2/rlike/tests/__init__.pyc
+${PYSITELIB}/rpy2/rlike/tests/__init__.pyo
+${PYSITELIB}/rpy2/rlike/tests/test_container.py
+${PYSITELIB}/rpy2/rlike/tests/test_container.pyc
+${PYSITELIB}/rpy2/rlike/tests/test_container.pyo
+${PYSITELIB}/rpy2/rlike/tests/test_functional.py
+${PYSITELIB}/rpy2/rlike/tests/test_functional.pyc
+${PYSITELIB}/rpy2/rlike/tests/test_functional.pyo
+${PYSITELIB}/rpy2/rlike/tests/test_indexing.py
+${PYSITELIB}/rpy2/rlike/tests/test_indexing.pyc
+${PYSITELIB}/rpy2/rlike/tests/test_indexing.pyo
+${PYSITELIB}/rpy2/robjects/__init__.py
+${PYSITELIB}/rpy2/robjects/__init__.pyc
+${PYSITELIB}/rpy2/robjects/__init__.pyo
+${PYSITELIB}/rpy2/robjects/conversion.py
+${PYSITELIB}/rpy2/robjects/conversion.pyc
+${PYSITELIB}/rpy2/robjects/conversion.pyo
+${PYSITELIB}/rpy2/robjects/functions.py
+${PYSITELIB}/rpy2/robjects/functions.pyc
+${PYSITELIB}/rpy2/robjects/functions.pyo
+${PYSITELIB}/rpy2/robjects/lib/__init__.py
+${PYSITELIB}/rpy2/robjects/lib/__init__.pyc
+${PYSITELIB}/rpy2/robjects/lib/__init__.pyo
+${PYSITELIB}/rpy2/robjects/lib/ggplot2.py
+${PYSITELIB}/rpy2/robjects/lib/ggplot2.pyc
+${PYSITELIB}/rpy2/robjects/lib/ggplot2.pyo
+${PYSITELIB}/rpy2/robjects/lib/grid.py
+${PYSITELIB}/rpy2/robjects/lib/grid.pyc
+${PYSITELIB}/rpy2/robjects/lib/grid.pyo
+${PYSITELIB}/rpy2/robjects/methods.py
+${PYSITELIB}/rpy2/robjects/methods.pyc
+${PYSITELIB}/rpy2/robjects/methods.pyo
+${PYSITELIB}/rpy2/robjects/numpy2ri.py
+${PYSITELIB}/rpy2/robjects/numpy2ri.pyc
+${PYSITELIB}/rpy2/robjects/numpy2ri.pyo
+${PYSITELIB}/rpy2/robjects/packages.py
+${PYSITELIB}/rpy2/robjects/packages.pyc
+${PYSITELIB}/rpy2/robjects/packages.pyo
+${PYSITELIB}/rpy2/robjects/robject.py
+${PYSITELIB}/rpy2/robjects/robject.pyc
+${PYSITELIB}/rpy2/robjects/robject.pyo
+${PYSITELIB}/rpy2/robjects/tests/__init__.py
+${PYSITELIB}/rpy2/robjects/tests/__init__.pyc
+${PYSITELIB}/rpy2/robjects/tests/__init__.pyo
+${PYSITELIB}/rpy2/robjects/tests/testArray.py
+${PYSITELIB}/rpy2/robjects/tests/testArray.pyc
+${PYSITELIB}/rpy2/robjects/tests/testArray.pyo
+${PYSITELIB}/rpy2/robjects/tests/testDataFrame.py
+${PYSITELIB}/rpy2/robjects/tests/testDataFrame.pyc
+${PYSITELIB}/rpy2/robjects/tests/testDataFrame.pyo
+${PYSITELIB}/rpy2/robjects/tests/testEnvironment.py
+${PYSITELIB}/rpy2/robjects/tests/testEnvironment.pyc
+${PYSITELIB}/rpy2/robjects/tests/testEnvironment.pyo
+${PYSITELIB}/rpy2/robjects/tests/testFormula.py
+${PYSITELIB}/rpy2/robjects/tests/testFormula.pyc
+${PYSITELIB}/rpy2/robjects/tests/testFormula.pyo
+${PYSITELIB}/rpy2/robjects/tests/testFunction.py
+${PYSITELIB}/rpy2/robjects/tests/testFunction.pyc
+${PYSITELIB}/rpy2/robjects/tests/testFunction.pyo
+${PYSITELIB}/rpy2/robjects/tests/testMethods.py
+${PYSITELIB}/rpy2/robjects/tests/testMethods.pyc
+${PYSITELIB}/rpy2/robjects/tests/testMethods.pyo
+${PYSITELIB}/rpy2/robjects/tests/testNumpyConversions.py
+${PYSITELIB}/rpy2/robjects/tests/testNumpyConversions.pyc
+${PYSITELIB}/rpy2/robjects/tests/testNumpyConversions.pyo
+${PYSITELIB}/rpy2/robjects/tests/testPackages.py
+${PYSITELIB}/rpy2/robjects/tests/testPackages.pyc
+${PYSITELIB}/rpy2/robjects/tests/testPackages.pyo
+${PYSITELIB}/rpy2/robjects/tests/testRObject.py
+${PYSITELIB}/rpy2/robjects/tests/testRObject.pyc
+${PYSITELIB}/rpy2/robjects/tests/testRObject.pyo
+${PYSITELIB}/rpy2/robjects/tests/testRobjects.py
+${PYSITELIB}/rpy2/robjects/tests/testRobjects.pyc
+${PYSITELIB}/rpy2/robjects/tests/testRobjects.pyo
+${PYSITELIB}/rpy2/robjects/tests/testVector.py
+${PYSITELIB}/rpy2/robjects/tests/testVector.pyc
+${PYSITELIB}/rpy2/robjects/tests/testVector.pyo
+${PYSITELIB}/rpy2/robjects/vectors.py
+${PYSITELIB}/rpy2/robjects/vectors.pyc
+${PYSITELIB}/rpy2/robjects/vectors.pyo
+${PYSITELIB}/rpy2/rpy_classic.py
+${PYSITELIB}/rpy2/rpy_classic.pyc
+${PYSITELIB}/rpy2/rpy_classic.pyo
+${PYSITELIB}/rpy2/tests.py
+${PYSITELIB}/rpy2/tests.pyc
+${PYSITELIB}/rpy2/tests.pyo
+${PYSITELIB}/rpy2/tests_rpy_classic.py
+${PYSITELIB}/rpy2/tests_rpy_classic.pyc
+${PYSITELIB}/rpy2/tests_rpy_classic.pyo
diff --git a/math/py-rpy/distinfo b/math/py-rpy/distinfo
index 28c79f6d821..4b9015b6321 100644
--- a/math/py-rpy/distinfo
+++ b/math/py-rpy/distinfo
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.8 2010/02/15 16:32:20 joerg Exp $
+$NetBSD: distinfo,v 1.9 2010/06/09 21:04:26 markd Exp $
 
-SHA1 (rpy-0.99.0.tar.gz) = 6b94e20adb555b9dfb914ef89745e75f3e9e4c8b
-RMD160 (rpy-0.99.0.tar.gz) = 9880e9da9d8b8cacccd947df906e643b7457aa44
-Size (rpy-0.99.0.tar.gz) = 79120 bytes
-SHA1 (patch-aa) = e148451a16e1d89bc26b4e86670772c626d24d69
+SHA1 (rpy2-2.1.3.tar.gz) = cf067b0fbcc9589b442538ee89273e61973c6207
+RMD160 (rpy2-2.1.3.tar.gz) = fb9354770fbbda39e07603f616bd9852f9573bc8
+Size (rpy2-2.1.3.tar.gz) = 127887 bytes
+SHA1 (patch-aa) = 5379b7bb276991e5180ef58ce0f721524603ed9b
diff --git a/math/py-rpy/patches/patch-aa b/math/py-rpy/patches/patch-aa
index d3f6dafe6ac..24b0a1019f9 100644
--- a/math/py-rpy/patches/patch-aa
+++ b/math/py-rpy/patches/patch-aa
@@ -1,13 +1,33 @@
-$NetBSD: patch-aa,v 1.5 2010/02/15 16:32:20 joerg Exp $
+$NetBSD: patch-aa,v 1.6 2010/06/09 21:04:26 markd Exp $
 
---- rpy_tools.py.orig	2006-06-20 19:22:37.000000000 +0000
-+++ rpy_tools.py
-@@ -93,7 +93,7 @@ def get_R_VERSION(RHOME=None, force_exec
-     if stat or len(output)<=0:
-       raise RuntimeError("Couldn't execute the R interpreter" +
-                          " `%s'.\n" % rexec )
--    version = re.search("R +([0-9]\.[0-9]\.[0-9])", output)
-+    version = re.search("R version +([0-9]+\.[0-9]+\.[0-9]+)", output)
-     if not version:
-       raise RuntimeError("Couldn't obtain version number from output\n"
-                                "of `R --version'.\n")
+--- setup.py.orig	2010-05-16 12:23:30.000000000 +0000
++++ setup.py
+@@ -1,4 +1,11 @@
+ 
+ import os, os.path, sys, shutil, re, itertools
++import distutils.sysconfig
++old_customize_compiler = distutils.sysconfig.customize_compiler
++def customize_compiler(compiler):
++    old_customize_compiler(compiler)
++    compiler.set_executables(linker_so=os.environ['FC'] + ' -shared')
++distutils.sysconfig.customize_compiler = customize_compiler
++
+ from distutils.command.build_ext import build_ext as _build_ext
+ from distutils.command.build import build as _build
+@@ -133,7 +140,7 @@ class build_ext(_build_ext):
+                         get_rconfig(r_home, 'BLAS_LIBS')
+ 
+         for e in self.extensions:
+-            e.extra_compile_args.extend(extra_link_args)
++            e.extra_link_args.extend(extra_link_args)
+ 
+     def run(self):
+         _build_ext.run(self)
+@@ -180,6 +187,7 @@ def get_rconfig(r_home, about, allow_emp
+     #sanity check of what is returned into rconfig
+     rconfig_m = None
+     possible_patterns = ('^(-L.+) (-l.+)$',
++                         '^(-Wl,-R.+) (-L.+) (-l.+)$',
+                          '^(-l.+)$',  # fix for the case -lblas is returned
+                          '^(-F.+? -framework .+)$', # fix for MacOS X
+                          '^(-framework .+)$',