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2015-11-03Add SHA512 digests for distfiles for math categoryagc1-1/+2
Problems found locating distfiles: Package dfftpack: missing distfile dfftpack-20001209.tar.gz Package eispack: missing distfile eispack-20001130.tar.gz Package fftpack: missing distfile fftpack-20001130.tar.gz Package linpack: missing distfile linpack-20010510.tar.gz Package minpack: missing distfile minpack-20001130.tar.gz Package odepack: missing distfile odepack-20001130.tar.gz Package py-networkx: missing distfile networkx-1.10.tar.gz Package py-sympy: missing distfile sympy-0.7.6.1.tar.gz Package quadpack: missing distfile quadpack-20001130.tar.gz Otherwise, existing SHA1 digests verified and found to be the same on the machine holding the existing distfiles (morden). All existing SHA1 digests retained for now as an audit trail.
2015-04-14Remove more references to python-2.6.wiz1-5/+2
2015-04-13Removing python26. EOL'd quite some ago and discussed a couple times onrodent1-2/+1
tech-pkg@ and pkgsrc-users@.
2015-04-12Add py-sqlite3 dependency. Fixes last issue from PR 49817.wiz1-2/+4
Bump PKGREVISION.
2015-04-10Fix interpreter path in installed file.wiz1-1/+4
Bump PKGREVISION.
2015-04-10Fix packaging with py33. Disable for py26.wiz2-3/+16
2015-04-10Fix PLIST for python-2.x.wiz1-1/+2
2015-04-07Update to 2.5.6, in the hope it addresses PR 49817.wiz3-10/+52
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)
2014-05-13Requires PCRE.joerg1-1/+2
2014-02-26bulk build suggested readlinewiedi1-1/+2
2014-01-19Update to 2.3.0:wiz4-58/+42
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)
2012-09-11"user-destdir" is default these daysasau1-3/+1
2011-12-18If BLAS_LIBS comes back empty, run with it instead of detonating.dholland2-6/+16
This makes it build for me.
2011-09-14Fix build on SunOS.hans1-1/+3
2011-06-29Add missing LICENSE.alnsn1-1/+2
From README: RPy2 is subject to the Mozilla Public License Version 1.1 (the "License"); you may not use RPy2 except in compliance with the License. You may obtain a copy of the License at http://www.mozilla.org/MPL/ (or see the file MPL_LICENSE) Software distributed under the License is distributed on an "AS IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for the specific language governing rights and limitations under the License. The Original Code is the RPy2 python package, itself subdivived into subpackages and modules. All code is Copyright of the respective author(s). See the file AUTHORS for further details regarding authorship. Alternatively, RPy2 may be used under the terms of either the GNU General Public License Version 2 or later (the "GPL", see the file GPL_LICENSE), or the GNU Lesser General Public License Version 2.1 or later (the "LGPL", see the file LGPL_LICENSE), in which case the provisions of the GPL or the LGPL are applicable instead of those above. If you wish to allow use of your version of this file only under the terms of either the GPL or the LGPL, and not to allow others to use your version of this file under the terms of the MPL, indicate your decision by deleting the provisions above and replace them with the notice and other provisions required by the GPL or the LGPL. If you do not delete the provisions above, a recipient may use your version of this file under the terms of any one of the MPL, the GPL or the LGPL.
2010-07-30"fortran" -> "fortran77" except where it is clear that it isn't F77.asau1-2/+2
"fortran" is alias of "fortran77" for now, but it will change later.
2010-06-09Update py-rpy to 2.1.3markd4-45/+179
Works with recent R and recent python.
2010-02-15Deal with two digit R --version output. Still mark as broken because itjoerg3-5/+7
depends on a no-longer existing header.
2008-09-19Catch up with PLIST changes. Bump revision.joerg2-4/+4
2008-06-12Add DESTDIR support.joerg1-1/+3
2008-04-26Update to match R 2.7.0markd2-5/+5
2008-04-25Update PYTHON_VERSIONS_COMPATIBLEjoerg1-2/+1
- assume that Python 2.4 and 2.5 are compatible and allow checking for fallout. - remove PYTHON_VERSIONS_COMPATIBLE that are obsoleted by the 2.3+ default. Modify the others to deal with the removals.
2007-11-07Fix PLIST, bump PKGREVISION for the new R.markd2-4/+5
2007-03-14Update py-rpy to 0.99.0markd3-10/+15
New features: * Dramatically simplify the build process for Win32 * It is now possible to use setup.cfg to control various aspects of the build process. 'config.in' contains a template containing all available options and what they do. Bug fixes * RPy compiled with Numeric support will no longer crash when run with Numeric available. * Crash during import when R is missing from the registry * Problem using R Wavelets library with RPy * RPy does not build on OS X, easy fix * Plotting with RPy crashes Python Other * The rpy.py now communicates RHOME, RVER, RVERSION, RUSER from python to the _rpy module using environment variables. This avoids the need to have duplicate C code to obtain these values, and makes things both more maintainable and more robust.
2007-02-22Whitespace cleanup, courtesy of pkglint.wiz1-3/+3
Patch provided by Sergey Svishchev in private mail.
2006-06-20Catch up with R 2.3.1: different module name, different output ofjoerg4-7/+21
R --version, different dependency. Bump revision.
2006-06-02py-Numeric exists only for 2.2+.joerg1-1/+2
2006-04-06Over 1200 files touched but no revisions bumped :)reed1-2/+2
RECOMMENDED is removed. It becomes ABI_DEPENDS. BUILDLINK_RECOMMENDED.foo becomes BUILDLINK_ABI_DEPENDS.foo. BUILDLINK_DEPENDS.foo becomes BUILDLINK_API_DEPENDS.foo. BUILDLINK_DEPENDS does not change. IGNORE_RECOMMENDED (which defaulted to "no") becomes USE_ABI_DEPENDS which defaults to "yes". Added to obsolete.mk checking for IGNORE_RECOMMENDED. I did not manually go through and fix any aesthetic tab/spacing issues. I have tested the above patch on DragonFly building and packaging subversion and pkglint and their many dependencies. I have also tested USE_ABI_DEPENDS=no on my NetBSD workstation (where I have used IGNORE_RECOMMENDED for a long time). I have been an active user of IGNORE_RECOMMENDED since it was available. As suggested, I removed the documentation sentences suggesting bumping for "security" issues. As discussed on tech-pkg. I will commit to revbump, pkglint, pkg_install, createbuildlink separately. Note that if you use wip, it will fail! I will commit to pkgsrc-wip later (within day).
2006-03-04Point MAINTAINER to pkgsrc-users@NetBSD.org in the case where nojlam1-2/+2
developer is officially maintaining the package. The rationale for changing this from "tech-pkg" to "pkgsrc-users" is that it implies that any user can try to maintain the package (by submitting patches to the mailing list). Since the folks most likely to care about the package are the folks that want to use it or are already using it, this would leverage the energy of users who aren't developers.
2006-02-05Recursive revision bump / recommended bump for gettext ABI change.joerg1-2/+2
2006-01-27Whoops, I forgot to actually fix the PLIST when I last "fixed" this. Bumpmarkd2-4/+4
PKGREVISION again.
2006-01-04Name of .so file depends on version of R built against so fix PLISTmarkd1-1/+4
again and depend on the latest version of R. Bump PKGREVISION.
2005-12-19Fix PLIST problem seen in bulk builds.markd1-2/+2
2005-10-21update to 0.4.6drochner4-34/+14
changes: many bugfixes, some improvements in mapping R-Python objects
2005-04-11Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.tv1-2/+1
2005-02-23Add RMD160 digests in addition to SHA1 ones.agc1-1/+2
2004-11-21Find new location of libR.so. Bump PKGREVISION.markd3-6/+16
Fixes PR pkg/28371
2004-07-22add python as categoryrecht1-2/+2
ok'd a while back at pkgsrcCon by agc and wiz
2004-04-27Convert to buildlink3.snj1-4/+4
2003-12-04CHANGES IN RPy 0.3.1adam3-11/+14
-------------------- Fixed bugs o There was several memory leaks due to bad management of Python refcounts. o There was wrong synchronization of the thread running the R event loop and the calls to the R interpreter. o There was a bug with signal handling which caused segfault when 'Ctrl-C' were pressed. o The R event loop shouldn't be run in non-interactive sessions. o The i/o Python callbacks were wrong synchronized with the R event loop thread. New features o Added a rpy_version symbol.
2003-09-14hange extension.mk to also install optimized files for distutils packages.recht2-3/+5
Inspired by FreeBSD "ports". Fix the PLISTs accordingly. Also, while at it, remove now obsolete compileall.py calls in post-install targets and insure that extension.mk is in included before builinlinks of other Python modules. Discussed with/ok'ed by drochner@.
2003-07-17s/netbsd.org/NetBSD.org/grant1-2/+2
2003-06-02Use tech-pkg@ in favor of packages@ as MAINTAINER for orphaned packages.jschauma1-2/+2
Should anybody feel like they could be the maintainer for any of thewe packages, please adjust.
2002-12-10Initial import of py-rpy-0.3.markd5-0/+48
Package provided by Kent Polk <kent@goathill.org> in personal email. RPy is a very simple, yet robust, Python interface to the R Programming Language. It can manage all kinds of R objects and can execute arbitrary R functions (including the graphic functions). All the errors from the R language are converted to Python exceptions. Any modules that later were installed on the R system, can easily be used from within Python, without introducing any changes.
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