- Update to 2.1.3

Feature safe:	yes

7 files changed, 157 insertions, 67 deletions

diff --git a/math/rpy2/Makefile b/math/rpy2/Makefile
index 59139f2ba7c6..03a51c3477e2 100644
--- a/math/rpy2/Makefile
+++ b/math/rpy2/Makefile
@@ -6,13 +6,13 @@
 # $FreeBSD$
 #
 
-PORTNAME=	rpy
-PORTVERSION=	1.0.3
-PORTREVISION=	13
+PORTNAME=	rpy2
+PORTVERSION=	2.1.3
 CATEGORIES=	math
-MASTER_SITES=	SF
+MASTER_SITES=	CHEESESHOP \
+		SF
 
-MAINTAINER=	wenheping@gmail.com
+MAINTAINER=	wen@FreeBSD.org
 COMMENT=	Python interface to the R Programming Language
 
 BUILD_DEPENDS=	${PYTHON_SITELIBDIR}/numpy:${PORTSDIR}/math/py-numpy \
@@ -21,10 +21,8 @@ RUN_DEPENDS=	${BUILD_DEPENDS}
 
 USE_PYTHON=	yes
 USE_PYDISTUTILS=	yes
-MAKE_ENV=	LDFLAGS="-L${LOCALBASE}/lib/R/modules -L${LOCALBASE}/lib/R/lib"
 
 post-patch:
-	@${REINPLACE_CMD} -e 's,^statichere ,,' ${WRKSRC}/src/rpymodule.c
 	@${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|g' ${WRKSRC}/setup.py
 
 .include <bsd.port.mk>
diff --git a/math/rpy2/distinfo b/math/rpy2/distinfo
index d31b5e01bbb8..978af65afaf7 100644
--- a/math/rpy2/distinfo
+++ b/math/rpy2/distinfo
@@ -1,3 +1,3 @@
-MD5 (rpy-1.0.3.tar.gz) = 10fd4904f622e5647638817279933900
-SHA256 (rpy-1.0.3.tar.gz) = 4ad23632ddcb6318a1af27a7f64526c110d59cbd166a0338c929de952f33c48b
-SIZE (rpy-1.0.3.tar.gz) = 87009
+MD5 (rpy2-2.1.3.tar.gz) = 51544f516942b99f4825dbe776049b1c
+SHA256 (rpy2-2.1.3.tar.gz) = 624a742024c584ce0d215be65f48a47380b0e2ce5f9139db5e9bacde903597e6
+SIZE (rpy2-2.1.3.tar.gz) = 127887
diff --git a/math/rpy2/files/patch-rpy_tools.py b/math/rpy2/files/patch-rpy_tools.py
deleted file mode 100644
index 09f166003c77..000000000000
--- a/math/rpy2/files/patch-rpy_tools.py
+++ /dev/null
@@ -1,13 +0,0 @@
---- rpy_tools.py.orig	2009-12-29 09:42:02.000000000 +0800
-+++ rpy_tools.py	2009-12-29 09:42:41.000000000 +0800
-@@ -97,8 +97,8 @@
-     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(" +([0-9]\.[0-9]\.[0-9])", output)
-+    # edd 05 Apr 2006  version = re.search("R +([0-9]\.[0-9][0-9]\.[0-9])", output)
-+    version = re.search(" +([0-9]\.[0-9][0-9]\.[0-9])", output)
-     if not version:
-       raise RuntimeError("Couldn't obtain version number from output\n"
-                                "of `R --version'.\n")
diff --git a/math/rpy2/files/patch-setup.py b/math/rpy2/files/patch-setup.py
deleted file mode 100644
index 6cc97c1af08f..000000000000
--- a/math/rpy2/files/patch-setup.py
+++ /dev/null
@@ -1,13 +0,0 @@
---- 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"]
-     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']
-+                         'src', '%%LOCALBASE%%/lib/R/include' ]
-+        libraries=['R','R']
-         library_dirs = r_libs
-         runtime_libs = r_libs
-         extra_compile_args=["-shared"]
diff --git a/math/rpy2/files/patch-src-RPy.h b/math/rpy2/files/patch-src-RPy.h
deleted file mode 100644
index 333d43f91776..000000000000
--- a/math/rpy2/files/patch-src-RPy.h
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/RPy.h.orig	2008-12-17 16:53:19.000000000 +0800
-+++ src/RPy.h	2008-12-17 16:53:35.000000000 +0800
-@@ -74,7 +74,7 @@
- #  endif
- #endif  /* _WIN32 */
- 
--#include <Rdevices.h> /* must follow Graphics.h */
-+#include <Rembedded.h> /* must follow Graphics.h */
- 
- 
- /* Missing definitions from Rinterface.h or RStartup.h */
diff --git a/math/rpy2/pkg-descr b/math/rpy2/pkg-descr
index d0dfbb55b2bf..b797ef63f35c 100644
--- a/math/rpy2/pkg-descr
+++ b/math/rpy2/pkg-descr
@@ -5,4 +5,8 @@ R language are converted to Python exceptions. Any module that later were
 installed on the R system, can easily be used from within Python, without
 introducing any changes.
 
-WWW: http://rpy.sourceforge.net/
+rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface
+to R, a proposed high-level interface, including wrappers to graphical
+libraries, as well as R-like structures and functions. 
+
+WWW: http://rpy.sourceforge.net/rpy2.html
diff --git a/math/rpy2/pkg-plist b/math/rpy2/pkg-plist
index 4b845a5ecc9b..c8cc3d49663c 100644
--- a/math/rpy2/pkg-plist
+++ b/math/rpy2/pkg-plist
@@ -1,19 +1,144 @@
-%%PYTHON_SITELIBDIR%%/_rpy2110.so
-%%PYTHON_SITELIBDIR%%/rpy.py
-%%PYTHON_SITELIBDIR%%/rpy.pyc
-%%PYTHON_SITELIBDIR%%/rpy.pyo
-%%PYTHON_SITELIBDIR%%/rpy_io.py
-%%PYTHON_SITELIBDIR%%/rpy_io.pyc
-%%PYTHON_SITELIBDIR%%/rpy_io.pyo
-%%PYTHON_SITELIBDIR%%/rpy_version.py
-%%PYTHON_SITELIBDIR%%/rpy_version.pyc
-%%PYTHON_SITELIBDIR%%/rpy_version.pyo
-%%PYTHON_SITELIBDIR%%/rpy_options.py
-%%PYTHON_SITELIBDIR%%/rpy_options.pyc
-%%PYTHON_SITELIBDIR%%/rpy_options.pyo
-%%PYTHON_SITELIBDIR%%/rpy_tools.py
-%%PYTHON_SITELIBDIR%%/rpy_tools.pyc
-%%PYTHON_SITELIBDIR%%/rpy_tools.pyo
-%%PYTHON_SITELIBDIR%%/rpy_wintools.py
-%%PYTHON_SITELIBDIR%%/rpy_wintools.pyc
-%%PYTHON_SITELIBDIR%%/rpy_wintools.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/__init__.py
+%%PYTHON_SITELIBDIR%%/rpy2/__init__.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/__init__.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/images/rpy2_logo.png
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/__init__.py
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/__init__.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/__init__.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/rinterface.so
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/rpy_device.so
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/__init__.py
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/__init__.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/__init__.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_Device.py
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_Device.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_Device.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_EmbeddedR.py
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_EmbeddedR.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_EmbeddedR.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_Sexp.py
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_Sexp.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_Sexp.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpClosure.py
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpClosure.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpClosure.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpEnvironment.py
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpEnvironment.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpEnvironment.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpVector.py
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpVector.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpVector.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpVectorNumeric.py
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpVectorNumeric.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpVectorNumeric.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/__init__.py
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/__init__.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/__init__.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/container.py
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/container.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/container.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/functional.py
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/functional.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/functional.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/indexing.py
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/indexing.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/indexing.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/__init__.py
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/__init__.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/__init__.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_container.py
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_container.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_container.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_functional.py
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_functional.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_functional.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_indexing.py
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_indexing.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_indexing.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/__init__.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/__init__.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/__init__.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/conversion.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/conversion.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/conversion.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/functions.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/functions.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/functions.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/__init__.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/__init__.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/__init__.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/ggplot2.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/ggplot2.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/ggplot2.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/grid.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/grid.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/grid.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/methods.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/methods.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/methods.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/numpy2ri.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/numpy2ri.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/numpy2ri.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/packages.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/packages.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/packages.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/robject.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/robject.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/robject.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/__init__.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/__init__.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/__init__.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testArray.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testArray.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testArray.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testDataFrame.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testDataFrame.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testDataFrame.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testEnvironment.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testEnvironment.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testEnvironment.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testFormula.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testFormula.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testFormula.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testFunction.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testFunction.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testFunction.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testMethods.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testMethods.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testMethods.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testNumpyConversions.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testNumpyConversions.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testNumpyConversions.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testPackages.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testPackages.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testPackages.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testRObject.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testRObject.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testRObject.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testRobjects.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testRobjects.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testRobjects.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testVector.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testVector.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testVector.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/vectors.py
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/vectors.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/robjects/vectors.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/rpy_classic.py
+%%PYTHON_SITELIBDIR%%/rpy2/rpy_classic.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/rpy_classic.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/tests.py
+%%PYTHON_SITELIBDIR%%/rpy2/tests.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/tests.pyo
+%%PYTHON_SITELIBDIR%%/rpy2/tests_rpy_classic.py
+%%PYTHON_SITELIBDIR%%/rpy2/tests_rpy_classic.pyc
+%%PYTHON_SITELIBDIR%%/rpy2/tests_rpy_classic.pyo
+@dirrm %%PYTHON_SITELIBDIR%%/rpy2/images
+@dirrm %%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests
+@dirrm %%PYTHON_SITELIBDIR%%/rpy2/rinterface
+@dirrm %%PYTHON_SITELIBDIR%%/rpy2/rlike/tests
+@dirrm %%PYTHON_SITELIBDIR%%/rpy2/rlike
+@dirrm %%PYTHON_SITELIBDIR%%/rpy2/robjects/lib
+@dirrm %%PYTHON_SITELIBDIR%%/rpy2/robjects/tests
+@dirrm %%PYTHON_SITELIBDIR%%/rpy2/robjects
+@dirrm %%PYTHON_SITELIBDIR%%/rpy2