From 5eaff8bbb478fe7bfa000c43a10a4b501f777c8c Mon Sep 17 00:00:00 2001 From: wiz Date: Tue, 7 Apr 2015 22:14:18 +0000 Subject: [PATCH] Update to 2.5.6, in the hope it addresses PR 49817. Release 2.5.6 ============= Bugs fixed ---------- - Detection of the R version during setup on Win8 (issues #255 and #258) - Segmentation fault when converting :mod:`pandas` :class:`Series` with elements of type object (issue #264) - The default converter from Python (non-rpy2) objects to rinterface-level objects was producing robjects-level objects whenever the input was of type :class:`list` (discovered while fixing issue #264) - Implemented suggested fix for issue with unlinking files on Windows (issue #191) - Testing rpy2 in the absence of ipython no longer stops with an error (issue #266) Release 2.5.5 ============= Bugs fixed ---------- - Crash (segfault) when querying an R object in an R environment triggers an error (symbol exists, but associated values resolves to an error - issue #251) - Change in the signature of `rcall` was not updated in the documentation (issue #259) - Minor update to the documentation (issue #257) Release 2.5.4 ============= Bugs fixed ---------- - Filter PNG files on size, preventing empty files causing trouble to be ipython notebook rendering of graphics later on (slight modification of the pull request #39) - Fix installation left unresolved with rpy2-2.5.3 (issue #248) - Possible segfault with Python 3.4 (issue #249) Release 2.5.3 ============= Changes ------- - `setup.py` has `install_requires` in addition to `requires` in the hope to fix the missing dependency with Python 2 (:mod:`singledispatch` is required but not installed). Bugs fixed ---------- - Extracting configuration information from should now work when R is emitting a warning (issue #247) - On OS X the library discovery step can yield nothing (see issue #246). A tentative fix is to issue a warning and keep moving. Release 2.5.2 ============= Bugs fixed ---------- - String representation of :class:`robjects.R` (issue #238) - Check during `build_ext` if unsupported version of R (pull request #32) - HTMl display of columns of factors in a DataFrame (issue #236) - HTML display of factors (issue #242) Release 2.5.1 ============= Bugs fixed ---------- - Require singledispatch if Python 3.3 (issue #232) - Fixed bug when R spits out a warning when asked configuration information (issue #233) - Restored printing of compilation information when running `setup.py` - Fixed installation issue on some systems (issue #234) - Workaround obscure failure message from unittest if Python < 3.4 and :mod:`singledispatch` cannot be imported (issue #235) Release 2.5.0 ============= New features ------------ - Experimental alternative way to preserve R objects from garbage collection. This can be activated with `rinterface.initr(r_preservehash=True)` (default is `False`. - :class:`GGPlot` object getting a method :meth:`save` mirroring R's `ggplot2::ggsave()`. - The conversion system is now using generics/single dispatch. - New module :mod:`rpy2.ipython.html` with HTML display for rpy2 objects - [Experimental] New function :func:`robjects.methods.rs4instance_factory` to type RS4 objects with more specificity. Changes ------- - The script `setup.py` was rewritten for clarity and ease of maintenance. Now it only uses `setuptools`. Release 2.4.4 ============= Bugs fixed ---------- - Use `input` rather than `raw_input` in the default console callback with Python 3 (fixes issue #222) - Issues with conversions, pandas, and rmagic (fixes issue #218 and more) Release 2.4.3 ============= Bugs fixed ---------- - `geom_raster` was missing from `rpy2.robjects.lib.ggplot2` (pull request #30) - Fixed issue with SVG rendering in ipython notebook (issue #217) - Regression with `rx2()` introduced with new conversion (issue #219) - Fixed documentation (missing `import`) (issue #213) Release 2.4.2 ============= Bugs fixed ---------- - Assigning an R `DataFrame` into an environment was failing if the conversion for Pandas was activated. (Issue #207) Release 2.4.1 ============= Bugs fixed ---------- - :meth:`rpy2.ipython` fixed spurious output to notebook cells. Release 2.4.0 ============= Changes ------- - Conversion system slightly changed, with the optional conversions for :mod:`numpy` and :mod:`pandas` modified accordingly. The changes should only matter if using third-party conversion functions. - The Python 3 version is now a first class citizen. `2to3` is no longer used, and the code base is made directly compatible with Python. This lowers significantly the installation time with Python 3 (which matters when developping rpy2). - The default options to initialize R (`rpy2.rinterface.initoptions') are no longer `('rpy2', '--quiet', '--vanilla', '--no-save')` but now `('rpy2', '--quiet', '--no-save')`. - :class:`robjects.vectors.ListVector` can be instanciated from any objects with a method `items()` with the expectation that the method returns an iterable of (name, value) tuples, or even be an iterable of (name, value) tuples. New features ------------ - For instances of :class:`rpy2.robjects.Function`, the `__doc__` is now a property fetching information about the parameters in the R signature. - Convenience function :func:`rpy2.robjects.packages.data` to extract the datasets in an R pacakges - :mod:`ipython`'s `rmagic` is now part of :mod:`rpy`. To use, `%load_ext rpy2.ipython` from within IPython. - new method :meth:`rpy2.rinterface.SexpEnvironment.keys`, returnings the names in the environment as a tuple of Python strings. - convenience class :class:`robjects.packages.InstalledPackages`, with a companion function :func:`robjects.packages.isinstalled`. - new class :class:`rinterface.SexpSymbol` to represent R symbols Bugs fixed ---------- - :meth:`rpy2.rinterface.Sexp.do_slot` was crashing when the parameter was an empty string (PR #155) Release 2.3.10 ============== Bugs fixed ---------- - `setup.py build` was broken when new R compiled with OpenMP (Issue #183) Release 2.3.9 ============= - Changes in pandas 0.13.0 broke the rpy2 conversion layer (Issue #173) Release 2.3.8 ============= Bugs fixed ---------- - Crash with R-3.0.2. Changes in R-3.0.2's C API coupled to a strange behaviour with R promises caused the problem. (PR #150) Release 2.3.7 ============= Bugs fixed ---------- - ggplot2's "guides" were missing - ggplot2's "theme_classic" was missing (PR #143) - ggplot2's "element_rect" was missing (PR #144) - :func:`rpy2.interactive.packages` was broken (PR #142) Release 2.3.6 ============= Bugs fixed ---------- - Several reports of segfault on OS X (since rpy2-2.3.1 - PR #109) - More fixes in converting `DataFrames` with dates from `pandas` Relase 2.3.5 ============ Bugs fixed ---------- - Missing mapping to ggplot2's `scale_shape_discrete` function - Better handling of dates in Pandas - Constructor for POSIXct improved (and fixed) Changes ------- - The attribute :attr:`rclass` is no longer read-only and can be set (since R allows it) - Importing the module :mod:`rpy2.interactive` no longer activates event processing by default (triggering concurrency errors when used with ipython). New features ------------ - New module :mod:`rpy2.interactive.ipython` (so far plotting automatically a ggplot2 figure in the iPython's console) - It is now possible to set the :attr:`rclass`. Relase 2.3.4 ============ Bugs fixed ---------- - Spurious error when running unit tests with Python 3 and numpy installed - Missing mapping to ggplot2's `geom_dotplot` function - Warnings are not longer printed (see Changes below) Changes ------- - Bumped target version of ggplot2 to 0.9.3.1 - Warnings are not longer printed. The C-level function in R became hidden in R-3.0, and the cost of an R-level check/print is relatively high if the R code called is very short. This might evolve into printing warnings only if interactive mode in Python (if this can be checked reliably). Release 2.3.3 ============= Bugs fixed ---------- - Some of the data.frames converted from :mod:`pandas` were triggering a :class:`TypeError` when calling :func:`repr` - In :mod:`rpy2.robjects.lib.ggplot2`, a mapping to `coord_fixed` was missing (PR #120) - Using the parameter `lib_loc` in a call to :func:`rpy2.robjects.packages.importr` was resulting in an error (PR #119) - Creating a `layer` through the `rpy2.robjects.lib.ggplot2` interface did not accept parameters (PR #122) - Testing the Python version was crashing of a number of unsupported Python versions (<= 2.6) (PR #117) New features ------------ - New module pandas2ri to convert from mod:`pandas` `DataFrame` objects - New classes :class:`rpy2.robjects.lib.grid.Unit` and :class:`rpy2.robjects.lib.grid.Gpar` to model their counterparts in R's `grid` package as they were previously missing from rpy2. Release 2.3.2 ============= Bug fixed --------- - Building on Win64 (pull request #6) - Fetching data from an R package through `importr` was masking any R object called `data` in that package. The data are now under the attribute name `__rdata__`. This is not completely safe either, although much less likely, a warning will be issued if still masking anything. Changes ------- - More informative error message when failing to build because `R CMD config` does not return what is expected Release 2.3.1 ============= Bugs fixed ---------- - default console print callback with Python (issue #112 linked to it) - deprecation warnings with ggplot2 (issue #111 and contributed patch) --- math/py-rpy/Makefile | 8 ++++---- math/py-rpy/PLIST | 46 ++++++++++++++++++++++++++++++++++++++++++-- math/py-rpy/distinfo | 8 ++++---- 3 files changed, 52 insertions(+), 10 deletions(-) diff --git a/math/py-rpy/Makefile b/math/py-rpy/Makefile index d7a6530a30a7e..c940ffc95cd5f 100644 --- a/math/py-rpy/Makefile +++ b/math/py-rpy/Makefile @@ -1,9 +1,9 @@ -# $NetBSD: Makefile,v 1.33 2014/05/13 17:09:21 joerg Exp $ +# $NetBSD: Makefile,v 1.34 2015/04/07 22:14:18 wiz Exp $ -DISTNAME= rpy2-2.3.0 +DISTNAME= rpy2-2.5.6 PKGNAME= ${PYPKGPREFIX}-${DISTNAME:S/rpy2/rpy/} CATEGORIES= math python -MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=rpy/} +MASTER_SITES= https://pypi.python.org/packages/source/r/rpy2/ MAINTAINER= pkgsrc-users@NetBSD.org HOMEPAGE= http://rpy.sourceforge.net/ @@ -18,7 +18,7 @@ LDFLAGS.SunOS+= -mimpure-text .include "../../devel/pcre/buildlink3.mk" .include "../../mk/readline.buildlink3.mk" -.include "../../lang/python/distutils.mk" +.include "../../lang/python/egg.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 6cd41751bc6a9..1c82184161a0a 100644 --- a/math/py-rpy/PLIST +++ b/math/py-rpy/PLIST @@ -1,17 +1,41 @@ -@comment $NetBSD: PLIST,v 1.13 2014/01/19 22:50:43 wiz Exp $ -${PYSITELIB}/${EGG_FILE} +@comment $NetBSD: PLIST,v 1.14 2015/04/07 22:14:18 wiz Exp $ +${PYSITELIB}/${EGG_INFODIR}/PKG-INFO +${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt +${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt +${PYSITELIB}/${EGG_INFODIR}/top_level.txt ${PYSITELIB}/rpy2/__init__.py ${PYSITELIB}/rpy2/__init__.pyc ${PYSITELIB}/rpy2/__init__.pyo ${PYSITELIB}/rpy2/interactive/__init__.py ${PYSITELIB}/rpy2/interactive/__init__.pyc ${PYSITELIB}/rpy2/interactive/__init__.pyo +${PYSITELIB}/rpy2/interactive/packages.py +${PYSITELIB}/rpy2/interactive/packages.pyc +${PYSITELIB}/rpy2/interactive/packages.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/ipython/__init__.py +${PYSITELIB}/rpy2/ipython/__init__.pyc +${PYSITELIB}/rpy2/ipython/__init__.pyo +${PYSITELIB}/rpy2/ipython/ggplot.py +${PYSITELIB}/rpy2/ipython/ggplot.pyc +${PYSITELIB}/rpy2/ipython/ggplot.pyo +${PYSITELIB}/rpy2/ipython/html.py +${PYSITELIB}/rpy2/ipython/html.pyc +${PYSITELIB}/rpy2/ipython/html.pyo +${PYSITELIB}/rpy2/ipython/rmagic.py +${PYSITELIB}/rpy2/ipython/rmagic.pyc +${PYSITELIB}/rpy2/ipython/rmagic.pyo +${PYSITELIB}/rpy2/ipython/tests/__init__.py +${PYSITELIB}/rpy2/ipython/tests/__init__.pyc +${PYSITELIB}/rpy2/ipython/tests/__init__.pyo +${PYSITELIB}/rpy2/ipython/tests/test_rmagic.py +${PYSITELIB}/rpy2/ipython/tests/test_rmagic.pyc +${PYSITELIB}/rpy2/ipython/tests/test_rmagic.pyo ${PYSITELIB}/rpy2/rinterface/__init__.py ${PYSITELIB}/rpy2/rinterface/__init__.pyc ${PYSITELIB}/rpy2/rinterface/__init__.pyo @@ -38,6 +62,9 @@ ${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_SexpSymbol.py +${PYSITELIB}/rpy2/rinterface/tests/test_SexpSymbol.pyc +${PYSITELIB}/rpy2/rinterface/tests/test_SexpSymbol.pyo ${PYSITELIB}/rpy2/rinterface/tests/test_SexpVector.py ${PYSITELIB}/rpy2/rinterface/tests/test_SexpVector.pyc ${PYSITELIB}/rpy2/rinterface/tests/test_SexpVector.pyo @@ -98,6 +125,12 @@ ${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/lib/tests/__init__.py +${PYSITELIB}/rpy2/robjects/lib/tests/__init__.pyc +${PYSITELIB}/rpy2/robjects/lib/tests/__init__.pyo +${PYSITELIB}/rpy2/robjects/lib/tests/test_ggplot2.py +${PYSITELIB}/rpy2/robjects/lib/tests/test_ggplot2.pyc +${PYSITELIB}/rpy2/robjects/lib/tests/test_ggplot2.pyo ${PYSITELIB}/rpy2/robjects/methods.py ${PYSITELIB}/rpy2/robjects/methods.pyc ${PYSITELIB}/rpy2/robjects/methods.pyo @@ -107,6 +140,12 @@ ${PYSITELIB}/rpy2/robjects/numpy2ri.pyo ${PYSITELIB}/rpy2/robjects/packages.py ${PYSITELIB}/rpy2/robjects/packages.pyc ${PYSITELIB}/rpy2/robjects/packages.pyo +${PYSITELIB}/rpy2/robjects/packages_utils.py +${PYSITELIB}/rpy2/robjects/packages_utils.pyc +${PYSITELIB}/rpy2/robjects/packages_utils.pyo +${PYSITELIB}/rpy2/robjects/pandas2ri.py +${PYSITELIB}/rpy2/robjects/pandas2ri.pyc +${PYSITELIB}/rpy2/robjects/pandas2ri.pyo ${PYSITELIB}/rpy2/robjects/robject.py ${PYSITELIB}/rpy2/robjects/robject.pyc ${PYSITELIB}/rpy2/robjects/robject.pyo @@ -143,6 +182,9 @@ ${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/testPandasConversions.py +${PYSITELIB}/rpy2/robjects/tests/testPandasConversions.pyc +${PYSITELIB}/rpy2/robjects/tests/testPandasConversions.pyo ${PYSITELIB}/rpy2/robjects/tests/testRObject.py ${PYSITELIB}/rpy2/robjects/tests/testRObject.pyc ${PYSITELIB}/rpy2/robjects/tests/testRObject.pyo diff --git a/math/py-rpy/distinfo b/math/py-rpy/distinfo index 53bb6fd4fef9e..a40b43009499e 100644 --- a/math/py-rpy/distinfo +++ b/math/py-rpy/distinfo @@ -1,5 +1,5 @@ -$NetBSD: distinfo,v 1.11 2014/01/19 22:50:43 wiz Exp $ +$NetBSD: distinfo,v 1.12 2015/04/07 22:14:18 wiz Exp $ -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 +SHA1 (rpy2-2.5.6.tar.gz) = d4a664b21b61b12608d9ff6714a087b43039e89e +RMD160 (rpy2-2.5.6.tar.gz) = ea13cf5379c025bbd7f8654c2cad0037196cf7a1 +Size (rpy2-2.5.6.tar.gz) = 165070 bytes