Update to 2.3.0:

Release 2.3.0
=============

New Features
------------

:mod:`rpy2.rinterface`:

- C-level API, allowing other C-level modules to make use of utilities
  without going through the Python level. The exact definition of
  the API is not yet fixed. For now there is
  PyRinteractive_IsInitialized() to assess whether R was initialized
  (through :mod:`rpy2.rinterface` or not).

- C-module _rpy_device, allowing one to implement R graphical devices
  in Python [(very) experimental]

- Tracking of R objects kept protected from garbage collection by rpy2
  is now possible.

- New method :meth:`Sexp.rid` to return the identifier of the R object
  represented by a Python/rpy2 object

:mod:`rpy2.rinteractive`:

- Dynamic build of Python docstrings out of the R manual pages

:mod:`rpy2.robjects.help`:

- Build dynamic help

:mod:`rpy2.robjects.packages:

- Build anonymous R packages from strings

- When using :func:`importr`, the datasets are added as an attribute
  :attr:`data`, itself an instance of a new class :class:`PackageData`.
  It no longer possible to access datasets are regular objects from
  a code package (because of changes in R), and the new system is
  more robust against quirks.

Changes
-------

:mod:`rpy2.rinterface`:

- :attr:`SexpClosure.env` to replace the method `closureenv`.


Release 2.2.6
=============

Bugs fixed
----------

- Newest R-2.15 and ggplot2 0.9 broke the ggplot2 interaface
  in :mod:`rpy2.robjects.lib.ggplot2`


Release 2.2.5
=============

Bugs fixed
----------

- install process: Library location for some of the R installations

- should compile on win32 (thanks to a patch from Evgeny Cherkashin),
   a work to a limited extend


Release 2.2.4
=============

Bugs fixed
----------

- Memory leak when creating R vectors from Python (issue #82)

Release 2.2.3
=============

Bugs fixed
----------

- Dynamic construction of S4 classes was looking for R help as 'class.<class>'
  rather than '<class>-class'

- The cleanup of temporary directories created by R was not happening if
  the Python process terminated without calline :func:`rpy2.rinterface.endr()`
  (issue #68, and proof-of-principle fix by chrish42)


Release 2.2.2
=============

Bugs fixed
----------

- With the robjects layer, repr() on a list containing non-vector elements
  was failing

Release 2.2.1
=============

Bugs fixed
----------

- MANIFEST.in was missing from MANIFEST.in, required with Python 3


Release 2.2.0
=============

New Features
------------

- Support for Python 3, and for some of its features ported to Python 2.7

:mod:`rpy2.robjects`:

- :meth:`Environment.keys` to list the keys

- classes :class:`robjects.vectors.POSIXlt` and
  :class:`robjects.vectors.POSIXlt` to represent vectors of R
  dates/time

- :func:`packages.get_packagepath` to get the path to an R package

- module :mod:`rpy2.robjects.help` to expose the R help system to Python

- Metaclass utilities in :mod:`rpy2.robjects.methods`, allowing to reflect
  automatically R S4 classes as Python classes.

- :meth:`rpy2.robjects.vectors.FactorVector.iter_labels` to iterate over the labels

- :class:`rpy2.robjects.vectors.ListVector` to represent R lists.

- Constructor for :class:`rpy2.robjects.vectors.ListVector` and
  :class:`rpy2.robjects.vectors.DataFrame` accept any iterable at the condition
  that the elements iterated through also valid subscripts for it (e.g., given
  an iterable v, the following is valid:

  .. code-block:: python

     x[k] for x in v


:mod:`rpy2.rinterface`:

- :data:`NA_Complex` and :class:`NAComplexType` for missing complex values.

- :class:`SexpExtPtr` to represent R objects of type EXTPTR (external pointers).

- :func:`rpy2.rinterface.parse` to parse a string a R code

- :func:`rpy2.rinterface.rternalise` to wrap Python function as :class:`SexpClosure` that can
  be called by R just as it was a function of its own.

- :class:`rpy2.rinterface.RNULLType` for R's C-level NULL value and
  :class:`rpy2.rinterface.UnboundValueType` for R's C-level R_UnboundValue
  (both singletons).

- :meth:`rinterface.SexpVector.index`, of similar behaviour to :meth:`list.index`.

- :meth:`rpy2.rinterface.Sexp.list_attrs` to list the names of all R attributes
  for a given object.

- :class:`rpy2.rinterface.ByteSexpVector` to represent R 'raw' vectors.

- constant `R_LEN_T_MAX` to store what is the maximum length for a vector in R.

- tuple `R_VERSION_BUILD` to store the version of R rpy2 was built against

- getter :attr:`Sexp.rclass` to return the R class associated with an object

:mod:`rpy2.rlike`:

- :class:`container.OrdDict` get proper methods :meth:`keys` and `get`

:mod:`rpy2.interactive`:

- A new sub-package to provide utilities for interactive work, either for
  handling R interactive events or use Python for interactive programming
  (as often done with the R console)

Changes
-------

:mod:`rpy2.robjects`:

- NA_bool, NA_real, NA_integer, NA_character and NA_complex are now
  deprecated (and removed).
  NA_Logical, NA_Real, NA_Integer, NA_Character, NA_Complex should be used.

- :class:`rpy2.robjects.packages.Package` now inherits from :class:`types.ModuleType`

- classes representing R vector also inherit their type-specific
  rinterface-level counterpart.

- Importing the :class:`rpy2.robjects.numpy2ri` is no longer sufficient
  to active the conversion. Explicit activation is now needed; the function
  `activate` can do that.


:mod:`rpy2.rinterface`:

- :class:`IntSexpVector`, :class:`FloatSexpVector`,
  :class:`StrSexpVector`, :class:`BoolSexpVector`, :class:`ComplexSexpVector`
  are now defined at the C level, improving performances
  and memory footprint whenever a lot of instances are created.

Bugs fixed
----------

- Better and more explicit detection system for needed libraries when
  compiling rpy2 (ported to release 2.1.6)

- Long-standing issue with readline fixed (issue #10)


Release 2.1.9
=============

Bugs fixed
----------

- The R class in rpy2.robjects is now truly a singleton

- When using numpy 1.5 and Python >= 2.7, the exposed buffer for R numerical (double)
  vectors or arrays was wrong.


Release 2.1.8
=============

Bugs fixed
----------

- Fixed issue with R arrays with more than 2 dimensions and numpy arrays
  (issue #47 - backported from the branch 2.2.x).


Release 2.1.7
=============

Bugs fixed
----------

- More fixes for the automated detection of include and libraries at build time.


Release 2.1.6
=============

Bugs fixed
----------

- Further fixes in the automatic detection of includes and libraries
  needed to compile rpy2 against R. The detection code has
  been refactored (backport from the 2.2.x branch)


Release 2.1.5
=============

Bugs fixed
----------

- fixes the automatic detection of R_HOME/lib during building/compiling
  when R_HOME/lib is not in lib/ (issue #54)


Release 2.1.4
=============

New features
------------

- :mod:`rpy2.robjects.lib.ggplot2` now has the functions :func:`limits`,
  :func:`xlim`, :func:`ylim` exposed (patch contributed anonymously)

Bugs fixed
----------

- Install script when the BLAS library used by R is specified as a library
  file (patch by Michael Kuhn)

4 files changed, 42 insertions, 58 deletions

diff --git a/math/py-rpy/Makefile b/math/py-rpy/Makefile
index be2c20485e7..e1678f60bbd 100644
--- a/math/py-rpy/Makefile
+++ b/math/py-rpy/Makefile
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.30 2012/09/11 23:04:32 asau Exp $
-#
+# $NetBSD: Makefile,v 1.31 2014/01/19 22:50:43 wiz Exp $
 
-DISTNAME=	rpy2-2.1.3
-PKGNAME=	${PYPKGPREFIX}-rpy-2.1.3
+DISTNAME=	rpy2-2.3.0
+PKGNAME=	${PYPKGPREFIX}-${DISTNAME:S/rpy2/rpy/}
 CATEGORIES=	math python
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=rpy/}
 
@@ -11,14 +10,13 @@ HOMEPAGE=	http://rpy.sourceforge.net/
 COMMENT=	R interface for Python
 LICENSE=	mpl-1.1 OR gnu-gpl-v2 OR gnu-lgpl-v2.1
 
-PYDISTUTILSPKG=		YES
 USE_LANGUAGES+=		c fortran77
 
 BUILDLINK_API_DEPENDS.R+= R>=2.11.0
 
 LDFLAGS.SunOS+=		-mimpure-text
 
-.include "../../lang/python/extension.mk"
+.include "../../lang/python/distutils.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 91eb097450f..6cd41751bc6 100644
--- a/math/py-rpy/PLIST
+++ b/math/py-rpy/PLIST
@@ -1,13 +1,22 @@
-@comment $NetBSD: PLIST,v 1.12 2010/06/09 21:04:26 markd Exp $
+@comment $NetBSD: PLIST,v 1.13 2014/01/19 22:50:43 wiz Exp $
+${PYSITELIB}/${EGG_FILE}
 ${PYSITELIB}/rpy2/__init__.py
 ${PYSITELIB}/rpy2/__init__.pyc
 ${PYSITELIB}/rpy2/__init__.pyo
-${PYSITELIB}/rpy2/images/rpy2_logo.png
+${PYSITELIB}/rpy2/interactive/__init__.py
+${PYSITELIB}/rpy2/interactive/__init__.pyc
+${PYSITELIB}/rpy2/interactive/__init__.pyo
+${PYSITELIB}/rpy2/interactive/process_revents.py
+${PYSITELIB}/rpy2/interactive/process_revents.pyc
+${PYSITELIB}/rpy2/interactive/process_revents.pyo
+${PYSITELIB}/rpy2/interactive/tests/__init__.py
+${PYSITELIB}/rpy2/interactive/tests/__init__.pyc
+${PYSITELIB}/rpy2/interactive/tests/__init__.pyo
 ${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/_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
@@ -26,6 +35,9 @@ ${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_SexpExtPtr.py
+${PYSITELIB}/rpy2/rinterface/tests/test_SexpExtPtr.pyc
+${PYSITELIB}/rpy2/rinterface/tests/test_SexpExtPtr.pyo
 ${PYSITELIB}/rpy2/rinterface/tests/test_SexpVector.py
 ${PYSITELIB}/rpy2/rinterface/tests/test_SexpVector.pyc
 ${PYSITELIB}/rpy2/rinterface/tests/test_SexpVector.pyo
@@ -59,12 +71,24 @@ ${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/constants.py
+${PYSITELIB}/rpy2/robjects/constants.pyc
+${PYSITELIB}/rpy2/robjects/constants.pyo
 ${PYSITELIB}/rpy2/robjects/conversion.py
 ${PYSITELIB}/rpy2/robjects/conversion.pyc
 ${PYSITELIB}/rpy2/robjects/conversion.pyo
+${PYSITELIB}/rpy2/robjects/environments.py
+${PYSITELIB}/rpy2/robjects/environments.pyc
+${PYSITELIB}/rpy2/robjects/environments.pyo
 ${PYSITELIB}/rpy2/robjects/functions.py
 ${PYSITELIB}/rpy2/robjects/functions.pyc
 ${PYSITELIB}/rpy2/robjects/functions.pyo
+${PYSITELIB}/rpy2/robjects/help.py
+${PYSITELIB}/rpy2/robjects/help.pyc
+${PYSITELIB}/rpy2/robjects/help.pyo
+${PYSITELIB}/rpy2/robjects/language.py
+${PYSITELIB}/rpy2/robjects/language.pyc
+${PYSITELIB}/rpy2/robjects/language.pyo
 ${PYSITELIB}/rpy2/robjects/lib/__init__.py
 ${PYSITELIB}/rpy2/robjects/lib/__init__.pyc
 ${PYSITELIB}/rpy2/robjects/lib/__init__.pyo
@@ -104,6 +128,12 @@ ${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/testHelp.py
+${PYSITELIB}/rpy2/robjects/tests/testHelp.pyc
+${PYSITELIB}/rpy2/robjects/tests/testHelp.pyo
+${PYSITELIB}/rpy2/robjects/tests/testLanguage.py
+${PYSITELIB}/rpy2/robjects/tests/testLanguage.pyc
+${PYSITELIB}/rpy2/robjects/tests/testLanguage.pyo
 ${PYSITELIB}/rpy2/robjects/tests/testMethods.py
 ${PYSITELIB}/rpy2/robjects/tests/testMethods.pyc
 ${PYSITELIB}/rpy2/robjects/tests/testMethods.pyo
diff --git a/math/py-rpy/distinfo b/math/py-rpy/distinfo
index e05bea878d8..53bb6fd4fef 100644
--- a/math/py-rpy/distinfo
+++ b/math/py-rpy/distinfo
@@ -1,6 +1,5 @@
-$NetBSD: distinfo,v 1.10 2011/12/18 21:32:08 dholland Exp $
+$NetBSD: distinfo,v 1.11 2014/01/19 22:50:43 wiz Exp $
 
-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) = 5ea826e4ec3d09feb4249e94f17e9e3115f70abf
+SHA1 (rpy2-2.3.0.tar.gz) = 57756415b343bfb960f319b53e6387ddbd0e0d08
+RMD160 (rpy2-2.3.0.tar.gz) = f2c70f8f7b242686e04d19c055090d3eb08005a9
+Size (rpy2-2.3.0.tar.gz) = 178022 bytes
diff --git a/math/py-rpy/patches/patch-aa b/math/py-rpy/patches/patch-aa
deleted file mode 100644
index dc17299deb8..00000000000
--- a/math/py-rpy/patches/patch-aa
+++ /dev/null
@@ -1,43 +0,0 @@
-$NetBSD: patch-aa,v 1.7 2011/12/18 21:32:08 dholland Exp $
-
-- configure compiler for pkgsrc
-- allow BLAS_LIBS to be empty
-- handle extra_link_args correctly
-- accept pkgsrc-reported link args
-
---- setup.py.orig	2010-05-16 12:23:30.000000000 +0000
-+++ setup.py
-@@ -1,5 +1,12 @@
- 
- 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
- 
-@@ -130,10 +137,10 @@ class build_ext(_build_ext):
-         extra_link_args = get_rconfig(r_home, '--ldflags') +\
-             get_rconfig(r_home, 'LAPACK_LIBS', 
-                         allow_empty=True) +\
--                        get_rconfig(r_home, 'BLAS_LIBS')
-+                        get_rconfig(r_home, 'BLAS_LIBS', allow_empty=True)
- 
-         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 .+)$',