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Revision 1.54 / (download) - annotate - [select for diffs], Mon Oct 23 06:37:48 2023 UTC (5 weeks, 4 days ago) by wiz
Branch: MAIN
Changes since 1.53: +3 -3 lines
Diff to previous 1.53 (colored)

*: update for Python base package change

Instead of depending on one of the removed packages (that are now included
in the base Python packages), include to require
a Python version that supplies them.

Remove now included packages.


Revision 1.53 / (download) - annotate - [select for diffs], Tue Aug 1 23:20:49 2023 UTC (3 months, 4 weeks ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2023Q3-base, pkgsrc-2023Q3
Changes since 1.52: +2 -2 lines
Diff to previous 1.52 (colored)

*: remove more references to Python 3.7

Revision 1.52 / (download) - annotate - [select for diffs], Sat Jul 1 08:37:40 2023 UTC (5 months ago) by wiz
Branch: MAIN
Changes since 1.51: +3 -4 lines
Diff to previous 1.51 (colored)

*: restrict py-numpy users to 3.9+ in preparation for update

Revision 1.51 / (download) - annotate - [select for diffs], Tue Jan 4 20:54:16 2022 UTC (22 months, 3 weeks ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2023Q2-base, pkgsrc-2023Q2, pkgsrc-2023Q1-base, pkgsrc-2023Q1, pkgsrc-2022Q4-base, pkgsrc-2022Q4, pkgsrc-2022Q3-base, pkgsrc-2022Q3, pkgsrc-2022Q2-base, pkgsrc-2022Q2, pkgsrc-2022Q1-base, pkgsrc-2022Q1
Changes since 1.50: +2 -1 lines
Diff to previous 1.50 (colored)

*: bump PKGREVISION for users

They now have a tool dependency on py-setuptools instead of a DEPENDS

Revision 1.50 / (download) - annotate - [select for diffs], Thu Dec 30 13:05:38 2021 UTC (23 months ago) by adam
Branch: MAIN
Changes since 1.49: +1 -2 lines
Diff to previous 1.49 (colored)

Forget about Python 3.6

Revision 1.49 / (download) - annotate - [select for diffs], Fri Dec 17 10:15:20 2021 UTC (23 months, 2 weeks ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2021Q4-base, pkgsrc-2021Q4
Changes since 1.48: +14 -5 lines
Diff to previous 1.48 (colored)

py-rpy: update to 3.4.5.

Release 3.4.5


- The deprecation warning when using :func:`rpy2.robjects.lib.grid.activate`
  was missing (indirectly revealed through issue #804).

- The named argument `LINPACK` in :meth:`rpy2.robjects.vectors.Matrix.svd`
  is no longer present in R.

Bugs fixed

- SIGPIPE sent to a process running Python+rpy2 could result in a segfault.
  This was caused by an incorrect setting of R signal handlers (issue #809).

Release 3.4.4


- `RRuntimeError` exceptions raised while evaluating R code
  an R magic (ipython/jupyter) are now propagated (issue #792).

Release 3.4.3

New features

- :mod:`rpy2.robjects.lib.ggplot2` maps more functions in the
  R package (issue #767)

- Utility function :func:`rpy2.robjects.lib.ggplot2.dict2rvec`
  to convert a Python `Dict[str, str]` into an R named vector
  of strings.

Bugs fixed

- Calling mod:`rpy2.situation` to report on the environment no longer
  stops with an uncaught exception when no R home can be determined
  (issue #774)

- Converting pandas series with the older numpy types could result
  in an error (issue #781)

- Numpy converter was not properly turing R integer or float arrays
  into their numpy equivalent (issue #785)

- The HTML representation of R list without named element was
  incorrect (issue #787)

Release 3.4.2

Bugs fixed

- Multithreading during the initialization of the embedded R no longer
  triggers a fatal error (issue #729)


- :mod:`pytest` is now an optional package. Optional sets of packages are
  `numpy`, `pandas`, `test`, and `all` (all optional packages). They
  can be specified during the installation. For example
  `pip install rpy2[test]`. (issue #670)

Release 3.4.1

Bugs fixed

- The file `requirements.txt` was missing from the source distribution
  on pypi (issue #764).

Release 3.4.0

New Features

- The mapping of the R C API now includes `Rf_isSymbol()`.

- Singleton class :class:`rpy2.rinterface_lib.sexp.RVersion` to report
  the R version for the embedded R.

- :func:`rpy2.rinterface.local_context` to create a context manager
  to evaluate R code within a local environment.

- The `staticmethod` :meth:`rpy2.robjects.vectors.DateVector.isrinstance`
  will tell whether an R objects is an R `Date` array.


- The dynamic generation of docstrings for R man pages
  is now using R's `Rd2txt`.

- The :func:`rpy2.rinterface_lib._rinterface_capi._findVarInFrame`
  is replaced by the function
  (see fix to issue #710).

- The functions :func:`rpy2.robjects.numpy.activate()` and
  :func:`rpy2.robjects.pandas.activate()` are deprecated and will
  be removed in rpy2-3.5.0.

- :func:`rpy2.rinterface_lib.embedded.setinitialized` was renamed to
  :func:`rpy2.rinterface_lib.embedded._setinitialized` to indicate that
  one should not use it.

- :meth:`rpy2.robjects.lib.ggplot2.vars` to map the R function
  `ggplot2::vars` (issue #742).

- Report correctly the class of R matrix objects with R>=4.0: it is
  now `('matrix', 'array')`. With R<4.0 `('matrix')` is still reported.

- The conversion of R/rpy2 objects to python objects using R class name mapping
  is extended to more classes. The documentation about conversion covers the topic.

- If `R_NilValue` is not null when the initialization of the embedded R is attempted,
  it is now assumed that R was initialized through other means (e.g., an other C library in the
  same process) and the C-level initialization is be skipped.

- The conversion `rpy2py` is now working with any Python object inheriting
  from `_rinterface_capi.SupportsSEXP`.

Bugs fixed

- The C function `Rf_findVarInFrame()` in the R API can trigger
  in an R-level error, and while this is rare, when it does
  when embedded in Python it creates a segfault. Calls are
  now wrapped in `R_ToplevelExec()` to limit the propagation
  of R exceptions. This solved issue #710.

- More complete and correct mapping of R class names in

- Initializing the embedded R caused the loss of ability to use Ctrl-C
  to send SIGINT to a Python process (issue #723)

- :mod:`rpy2.sitation` is now working when the environment variable
  `R_HOME` is set even though R is not in the `PATH` or in the Windows
  registry (issue #744).

- Handling an R language objects could result in a segfault when its
  R class was queried (issue #749).

- The conversion of R string arrays to `numpy` arrays was leaving
  R's `NA` value as R NA objects. NAs in this type of arrays are now
  turned to `None` in the resulting `numpy` array (issue #751).

- `rpy2.situation.get_rlib_path()` was returning an environment variable
  with an invalid separator on Windows (mentioned in issue #754).

- R strings encoded with something else than 'utf-8' could result in
  errors when trying to convert to Python strings (issue #754).

- Extracting documentation pages for R objects in packages could
  generate spurious warnings when several "section" tags are present.

- R `Date` arrays/vectors were not wrapped into
  :class:`rpy2.robjects.vectors.DateVector` objects but left as
  R arrays of floats (which they are at the C level).

- The HTML representation of short R lists without names could
  fail with an error.

- The :meth:`__repr__` of `robjects`-level objects was not displaying
  the rpy2 class the R object is mapped to.

Release 3.3.6

Bugs fixed

- The unit tests for importing R packages with `lib_loc` were
  broken (issue #720).

- Trying to create a memoryview for an R array with complex values
  was failing with an attribute error.

- Fix the constructor of metaclass

- Fix call to end the embedded R in :class:`rpy2.robjects.R.__cleanup__`
  (issue #734).

Release 3.3.5

Bugs fixed

- The callback handler to read input to R returned an
  invalid result, leading to R asking for input
  without ever acknowledging it received it.

Release 3.3.4

Bugs fixed

- Creating an R vector object from a Python object implementing
  the buffer protocol could give incorrect results as C-level
  incompatibilities could be missed (issue #702).

- :func:`rpy2.robjects.packages.importr` could fail when `lib_loc`
  was specified (issue #705).

Release 3.3.3

Bugs fixed

- Fallback for when `str2lang` is missing (R < 3.6)

- Fix segfault with :meth:`PairListSexpVector.__getitem__` when
  elements of the R pairlist have a `NILSXP` name (issue #700)

Release 3.3.2

Bugs fixed

- Initial fixes to have rpy2 running in ABI mode on Windows.
  Few tests are not passing (many in callbacks for R's C API).

- System detection is now checking for FreeBSD.

Release 3.3.1

Bugs fixed

- :meth:`rpy2.robjects.conversion.NameClassMap.update` can update
  the mapping (:class:`dict`) or the default class.


- Adding local converters was overwriting the base `NameClassMap`.

Release 3.3.0

New features

- Trying to import an R package that is not installed will now raise an
  exception :class:`rpy2.robjects.packages.PackageNotInstalledError`.

- The R C API functions `void SET_FRAME(SEXP x, SEXP v)`,
  `void SET_ENCLOS(SEXP x, SEXP v)` and `void SET_HASHTAB(SEXP x, SEXP v)`
  are now accessible through rpy2.

- The module :mod:`rpy2.situation` can now return `LD_LIBRARY_PATH`
  information about R. For example with
  `python -m rpy2.situation LD_LIBRARY_PATH`

- :meth:`rpy2.robjects.methods.RS4.extends` lists the class names in the
  inheritance line.

- The conversion of R objects to Python allows much more flexibility
  and better allow the use of independent code converting different classes.
  This is currently limited to R objects that are lists, environments, or
  S4 objects. The Sphinx documentation contains an example. While this is
  still work in progress this should already address concerns
  at the origin of issue #539 about S4 classes.

- :class:`rpy2.robjects.language.LangVector` to map R language objects at
  the `robjects` level.

- :class:`rpy2.robjects.vectors.PairlistVector` to map R pairlist objects at
  the `robjects` level.

- An alternative function to display the output of R cells can be
  specified using `-d` or `--display` in the magic arguments
  (in :mod:`rpy2.ipython.rmagic`).

- Python classes representing underlying R objects no longer have to
  exclusively rely on inheritance from :mod:`rpy2.rinterface` objects`.
  An abstract class :class:`rpy2.rinterface_lib.sexp.SupportsSEXP` is added
  to identify objects supporting a `__sexp__` protocol, and that abstract
  class can also be used with type hints.
- :func:`rpy2.robjects.functions.wrap_r_functions` can create Python functions
  with matching signature from R functions

- :func:`rpy2.robjects.functions.wrap_r_functions` can create Python functions
  with matching signature from R functions.

- New class :class:`rpy2.rinterface_lib._rinterface_capi.UninitializedRCapsule`
  to allow the instanciation of "placeholder" rpy2 objects before the
  embedded R is initialized. This facilitate the use of static typing checks
  such as mypy, mocking for tests that do not involve the execution of R
  code, and allow cleaner implementations of module-level globals
  that are R objects.

- New class :class:`rpy2.robjects.vectors.DateVector` to represent R dates.

- :class:`pandas.Series` containing date objects can now be converted to R
  `Date` vectors.


- When calling R C-API's `R_ParseVector` and a error occurs, the
  exception message now contains the parsing status.

- :mod:`rpy2.rinterface_lib.embedded` has a module-level "constant"
  `DEFAULT_C_STACK_LIMIT` used when initializing the embedded R.

- When creating a :mod:`rpy2.robjects.vectors.DataFrame` from (name, vector)
  pairs, the names are no longer transformed to syntactically valid R
  symbols (issue #660).

- The value `nan` in :mod:`pandas` Series with strings is now converted
  to R NA (issue #668).

- Initial support for :const:`pandas.NA` (still experimental in pandas
  at the time of writing, and rpy2 support is limited to arrays of strings).

- :mod:`pandas` series of dtype :class:`pandas.StringDType`, experimental in pandas 1.0,
  are now supported by the converted (in the pandas-to-R direction) (issue #669)

- Version checking for the mapping of R packages in :mod:`rpy2.robjects.lib` is
  now more permissive (check that version prefixes are matching).

Bugs fixed

- Building ABI only mode could require an API build environment (and fail
  with an error when not present).

- SVG output for the R magic were incorrectly bytes objects.

- :meth:`rpy2.rinterface_lib.sexp.StrSexpVector.__getitem__` was returning the string
  `'NA'` when an R NA value. Not it returns `rpy2.rinterface_lib.na_values.NA_Character`.

Release 3.2.7

Bugs fixed

- An f-string in `` prevented installation
  on Python 3.5 (issue #654).

Release 3.2.6

Bugs fixed

- The conversion of date/time object with specified timezones
  was wrong when different than the local time zone (issue #634)

- Iterating over :mod:`rpy2.situation.iter_info()` could result
  in a error because of a typo in the code.


- :mod:`pandas` 1.0.0 breaks the conversion layer. A warning
  is now emitted whenever trying to use `pandas` >= 1.0.

Release 3.2.5

Bugs fixed

- Latest release for R package `rlang` broke import through `importr()`.
  A workaround for :mod:`rpy2.robjects.lib.ggplot2` is to rename the
  offending R object (issue #631).


- f-string requiring Python >= 3.6 removed.

Release 3.2.4

Bugs fixed

- An incomplete backport of the bug fixed in 3.2.3 broke the ABI mode.

Release 3.2.3

Bugs fixed

- Error when parsing strings as R codes could result in a segfault.

Release 3.2.2

Bugs fixed

- Python format error when trying to report that the system is not reported
  on Windows (issue #597).

- The setup script would error on build if R is not installed. It is now
  printing an error message.

Release 3.2.1

Bugs fixed

- The wrapper for the R package `dbplyr` could not import the underlying
  package (refactoring elsewhere was not propagated there).

- Creating R objects called `names` `globalenv` caused the method
  :meth:`Sexp.names` to fail (issue #587).

- Whenever the pandas conversion was activated :class:`FloatSexpVector` instances
  with the R class `POSIXct` attached where not corrected mapped back to pandas
  datetime arrays. (issue #594).

- Fix installation when an installation when a prefix without write access is used
  (issue #588).

Release 3.2.0

New features

- rpy2 can built and used with :mod:`cffi`'s ABI or API modes (releases 3.0.x and
  3.1.x were using the ABI mode exclusively). At the time of writing the default
  is still the ABI mode but the choice can be controlled through the environment variable
  `RPY2_CFFI_MODE`. If set, possible values are `ABI` (default if the environment
  variable is not set), `API`, or `BOTH`. When the latter, both `API` and `ABI`
  modes are built, and the choice of which one to use can be made at run time.


- The "consoleread" callback (reading input to the R console) is now assuming UTF-8
  (was previously assuming ASCII) and is no longer trying to add a "new line" character
  at the end of the input.

- Querying an R environment with an invalid key will generate a :class:`TypeError`
  or a :class:`ValueError` depending on the issue (rather than always :class:`ValueError`

Bugs fixed

- `` is now again compatible with Python2 (issue #580).

- Unit tests were failing if numpy is not installed.

- :mod:`rpy2.situation` is no longer breaking when R is not the in path and
  there is no environment variable `R_HOME`.

- Build script for the cffi interface is now using the environment
  variable `R_HOME` whenever defined (rather that always infer it from the
  R in the PATH).

- Converting R strings back to Python was incorrectly using `Latin1` while `UTF-8` was
  intended (issue #537).

Release 3.1.0

New features

- Python matrix multiplication (`__matmul__` / `@`) added to
  R :class:`Matrix` objects.

- An :class:`threading.RLock` is added to :mod:`rpy2.rinterface_lib.openrlib` and is
  used by the context manager :func:`rpy2.rinterface_lib.memorymanagement.rmemory`
  to ensure that protect/unprotect cycles cannot be broken by thread switching, at least
  as long as the context manager is used to handle such cycles (see issue #571).

- The documentation covers the use of notebooks (mainly Jupyter/Jupyterlab).

- The PNG output in Jupyter notebooks R cells can now specify an argument `--type`
  (passed as the named argument `type` in the R function `png`).
  For example on some Linux systems and R installations, the type `cairo`
  can fix issues when alpha transparency is used.


- Added callbacks for `ptr_R_Busy()` and `ptr_R_ProcessEvents()`.

- `rstart` now an objects in :mod:`rpy2.rinterface_lib.embedded`
  (set to `None` until R is initialized).

- Unit tests are included in a subpackage :mod:`rpy2.tests` as was the
  case before release 3.0.0 (issue #528).

- Experimental initialization for Microsoft Windows.

- :mod:`rpy2.situation` is now also reporting the rpy2 version.

- :func:`rpy2.robjecs.package_utils.default_symbol_check_after` was
  renamed  :func:`rpy2.robjecs.package_utils.default_symbol_resolve`.
  The named parameters `default_symbol_check_after` present in few methods
  in :mod:`rpy2.robjects.packages` and :mod:`rpy2.robjects.functions` were
  modified to keep a consistent naming.

- Trying to instantiate an :class:`rpy2.rlike.container.OrdDict` with a
  a :class:`dict` will result in a :class:`TypeError` rather than a

- Methods of :class:`rpy2.rlike.container.OrdDict` now raises a
  :class:`NotImplementedError` when not implemented.

- The creation of R vectors from Python sequences is now relying on a method
  :meth:`_populate_r_vector` that allows vectorized implementation to
  to improve speed.

- Continuous integration tests run against Python 3.6, 3.7, and 3.8. It is
  no longer checked against Python 3.5.

Bugs fixed

- `aes` in :mod:`rpy2.robjects.lib.ggplot2` had stopped working with the
  R package ggplot2 reaching version 3.2.0. (issue #562).

- Better handling of recent :mod:`pandas` arrays with missing values
  (related to issue #544).

- The mapping of the R operator `%in%` reachable through the attribute `ro`
  of R vectors was always returning `True`. It is now working properly.

- R POSIXct vectors with `NA` dates were triggering an error when converted
  in a data frame converted to :mod:`pandas` (issue #561).

Release 3.0.5

Bugs fixed

- No longer allow installation if Python 3 but < 3.5.

- Fixed error `undefined symbol: DATAPTR` if R < 3.5 (issue #565).

Release 3.0.4

Bugs fixed

- Fixed conversion of `pandas` :class:`Series` of dtype `pandas.Int32Dtype`,
  or `pandas.Int64Dtype` (issue #544).

Release 3.0.3

Bugs fixed

- Fixed the evaluation of R code using the "R magic" was delaying all
  output to the end of the execution of that code, independently of
  whether the attribute `cache_display_data` was `True` or `False`
  (issue #543).

- Fixed conversion of :class:`pandas.Series` of `dtype` "object" when
  all items are either all of the same type or are :obj:`None` (issue #540).

Release 3.0.2

Bugs fixed

- Failing to import `pandas` or `numpy` when loading the "R magic" extension
  for jupyter/ipython was hiding the cause of the error in the `ImportError`

- Fallback when an R `POSIXct` vector does not had an attribute `"tzone"`
  (issue #533).

- Callback for console reset was not set during R initialization.

- Fixed rternalized function returning rpy2 objects (issue #538).

- `--vanilla` is no longer among the default options used to initialize R
  (issue #534).

Release 3.0.1

Bugs fixed

- Script to install R packages for docker image never made it to version

- Conversion of R arrays/matrices into numpy object trigged a segfault
  during garbage collection (issue #524).

Release 3.0.0

New features

- rpy2 can be installed without a development environment.

- Unit tests are now relying on the Python module `pytest`.

- :attr:`rpy2.rinterface.NA_Integer` is now only defined when the embedded R
  is initialized.


- complete rewrite of :mod:`rpy2.rinterface`.
  :mod:`cffi` is now used to interface with the R compiled shared library.
  This allows ABI calls and removes the need to compile binaries. However, if
  compilation is available (when installing or preparing pre-compiled binaries)
  faster implementations of performance bottlenecks will be available.

- calling :func:`rpy2.rinterface.endr` multiple times is now only ending R
  the first time it is called (note: an ended R cannot successfully be

- The conversion system in the mod:`rpy2.robjects.conversion` now has only
  two conversions `py2rpy` and rpy2py`. `py2rpy` tries to convert any
  Python object into an object rpy2 can use with R and `rpy2py` tries
  to convert any rpy2 object into a either a non-rpy2 Python object or
  a mod:`rpy2.robjects` level object.

- The method `get` for R environments is now called `find()` to avoid
  confusion with the method of the same name in Python (:meth:`dict.get`).

- :class:`rpy2.robjects.vectors.Vector`, :class:`rpy2.robjects.vectors.Matrix`,
  and :class:`rpy2.robjects.vectors.Array` can no longer be used to create
  R arrays of unspecified type. New type-specific classes (for example for
  vectors :class:`rpy2.robjects.vectors.IntVector`,
  :class:`rpy2.robjects.vectors.ComplexVector`, or
  :class:`rpy2.robjects.vectors.StrVector`) should be used instead.

- mod:`rpy2.rpy_classic`, an implementation of the `rpy` interface using
  :mod:`rpy2.rinterface` is no longer available.

- :class:`rpy2.robjects.ParsedCode` and
  :class:`rpy2.robjects.SourceCode` are moved to
  :class:`rpy2.robjects.packages.ParsedCode` and

Bugs fixed

- Row names in R data frames were lost when converting to pandas data frames
  (issue #484).

Known issues

- Mismatch between R's POSIXlt `wday` and Python time struct_time's `tm_wday`
  (issue #523).

Release 2.9.6

Bugs fixed

- Latest release of :mod:`pandas` deprecated :meth:`DataFrame.from_items`.
  (issue #514).

- Latest release of :mod:`pandas` requires categories to be a list
  (not an other sequence).

Known issues

- The numpy buffer implemented by R arrays is broken for complex numbers

Release 2.9.5

Bugs fixed

- Missing values in pandas :class:`Category` series were creating
  invalid R factors when converted (issue #493).

Release 2.9.4

Bugs fixed

- Fallback for failure to import numpy or pandas is now dissociated from
  failure to import :mod:`numpy2ri` or :mod:`pandas2ri` (issue #463).

- :func:`repr` for R POSIX date/time vectors is now showing a string
  representation of the date/time rather than the timestamp as a float
  (issue #467).

- The HTML representation of R data frame (the default representation in the
  Jupyter notebook) was displaying an inconsistent number of rows
  (found while workin on issue #466).

- Handle time zones in timezones in Pandas when converting to R data frames
  (issue #454).

- When exiting the Python process, the R cleanup is now explicitly request
  to happen before Python's exit. This is preventing possible segfaults
  the process is terminating (issue #471).

- dplyr method `ungroup()` was missing from
  :class:`rpy2.robjects.lib.dplyr.DataFrame` (issue #473).

Release 2.9.3

Bugs fixed

- Delegate finding where is local time zone file to either a user-specified
  module-level variable `default_timezone` or to the third-party
  module :mod:`tzlocal` (issue #448).

Release 2.9.2


- The pandas converter is converting :class:`pandas.Series` of `dtype` `"O"`
  to :class:`rpy2.robjects.vectors.StrVector` objects, issueing a warning
  about it (See issue #421).

- The conversion of pandas data frame is now working with columns rather
  than rows (introduce in bug fix for issue #442 below) and this is expected
  to result in more efficient conversions.

Bugs fixed

- Allow floats in figure sizes for R magic (Pull request #63)

- Fixed pickling unpickling of robjects-level instances,
  regression introduced in fix for issue #432 with release 2.9.1 (issue #443).

- Fixed broken unit test for columns of `dtype` `"O"` in `pandas` data frames.

- Fixed incorrect conversion of R factors in data frames to columns of
  integers in pandas data frame (issue #442).

Revision 1.48 / (download) - annotate - [select for diffs], Tue Jun 29 08:42:01 2021 UTC (2 years, 5 months ago) by nia
Branch: MAIN
CVS Tags: pkgsrc-2021Q3-base, pkgsrc-2021Q3
Changes since 1.47: +2 -1 lines
Diff to previous 1.47 (colored)

py-numpy: "Python version >= 3.7 required."

Revision 1.47 / (download) - annotate - [select for diffs], Mon Oct 12 21:52:03 2020 UTC (3 years, 1 month ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2021Q2-base, pkgsrc-2021Q2, pkgsrc-2021Q1-base, pkgsrc-2021Q1, pkgsrc-2020Q4-base, pkgsrc-2020Q4
Changes since 1.46: +2 -2 lines
Diff to previous 1.46 (colored)

math/blas, math/lapack: Install interchangeable BLAS system

Install the new interchangeable BLAS system created by Thomas Orgis,
currently supporting Netlib BLAS/LAPACK, OpenBLAS, cblas, lapacke, and
Apple's Accelerate.framework.  This system allows the user to select any
BLAS implementation without modifying packages or using package options, by
setting PKGSRC_BLAS_TYPES in mk.conf. See mk/ for details.

This commit should not alter behavior of existing packages as the system
defaults to Netlib BLAS/LAPACK, which until now has been the only supported


Add new mk/ for inclusion in dependent packages
Install compatible Netlib math/blas and math/lapack packages
Update math/blas and math/lapack MAINTAINER approved by adam@
OpenBLAS, cblas, and lapacke will follow in separate commits
Update direct dependents to use mk/
Perform recursive revbump

Revision 1.46 / (download) - annotate - [select for diffs], Mon Aug 24 06:40:20 2020 UTC (3 years, 3 months ago) by tnn
Branch: MAIN
CVS Tags: pkgsrc-2020Q3-base, pkgsrc-2020Q3
Changes since 1.45: +3 -2 lines
Diff to previous 1.45 (colored)

py-rpy: seems to want pcre2, not pcre

Revision 1.45 / (download) - annotate - [select for diffs], Sun Jan 26 05:26:25 2020 UTC (3 years, 10 months ago) by rillig
Branch: MAIN
CVS Tags: pkgsrc-2020Q2-base, pkgsrc-2020Q2, pkgsrc-2020Q1-base, pkgsrc-2020Q1
Changes since 1.44: +2 -2 lines
Diff to previous 1.44 (colored)

all: migrate some SourceForge homepage URLs back from https to http

In the above commit, the homepage URLs were migrated from http to https,
assuming that SourceForge would use the same host names for both http and
https connections. This assumption was wrong. Their documentation at states
that the https URLs use the domain instead.

To make the homepages from the above commit reachable again, pkglint has
been extended to check for reachable homepages. This check is only
enabled when the --network command line option is given.

Each of the homepages that referred to https://$
before was migrated to https://$ (27), and if that
was not reachable, to the fallback URL http://$

Revision 1.44 / (download) - annotate - [select for diffs], Sat Jan 18 23:32:53 2020 UTC (3 years, 10 months ago) by rillig
Branch: MAIN
Changes since 1.43: +2 -2 lines
Diff to previous 1.43 (colored)

all: migrate several HOMEPAGEs to https

pkglint --only "https instead of http" -r -F

With manual adjustments afterwards since pkglint 19.4.4 fixed a few
indentations in unrelated lines.

This mainly affects projects hosted at SourceForce, as well as, CTAN and GNU.

Revision 1.43 / (download) - annotate - [select for diffs], Tue Nov 28 09:07:23 2017 UTC (6 years ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2019Q4-base, pkgsrc-2019Q4, pkgsrc-2019Q3-base, pkgsrc-2019Q3, pkgsrc-2019Q2-base, pkgsrc-2019Q2, pkgsrc-2019Q1-base, pkgsrc-2019Q1, pkgsrc-2018Q4-base, pkgsrc-2018Q4, pkgsrc-2018Q3-base, pkgsrc-2018Q3, pkgsrc-2018Q2-base, pkgsrc-2018Q2, pkgsrc-2018Q1-base, pkgsrc-2018Q1, pkgsrc-2017Q4-base, pkgsrc-2017Q4
Changes since 1.42: +4 -3 lines
Diff to previous 1.42 (colored)

py-rpy: updated to 2.9.1

Release 2.9.1

- Fixing issue 432 (see Section Bugs fixed below) involved removed the method
  `__reduce__` previously provided for all rpy2 objects representing R objects.

Bugs fixed
- An error when installing with an unsupported R version was fixed.
- The docstring for `rinterface.endr()` was improperly stating that the function was not taking
  any argument.
- Target version of dplyr and tidyr are now 0.7.4 and 0.7.2 respectively.
- Fixed memory leak when pickling objects. Fixing the leak caused a
  slight change in the API (see Section Changes above).
- Conversion to :mod:`pandas` now handling R ordered factor.
- :mod:`jinja2` was not listed as a dependency

Revision 1.42 / (download) - annotate - [select for diffs], Wed Oct 18 16:17:12 2017 UTC (6 years, 1 month ago) by adam
Branch: MAIN
Changes since 1.41: +7 -13 lines
Diff to previous 1.41 (colored)

py-rpy: update to 2.9.0

Release 2.9.0:

New features

- New module :mod:`rpy2.situation` to extract and report informations
  about the environment, such as where is the R HOME, what is the
  version of R, what is the version of R rpy2 was built with, etc...
  The module is also designed to be run directly and provide diagnostics:
  `python -m rpy2.situation`.

- :meth:`Environment.values`, :meth:`Environment.pop`,
  :meth:`Environment.popitems`, :meth:`Environment.clear`
  to match :meth:`dict.values`,
  :meth:`dict.pop`, :meth:`dict.popitems`, :meth:`dict.clear`.

- :class:`VectorOperationsDelegator` now has a method `__matmul__` to implement
  Python's matrix multiplication operator (PEP-0645).

- A rule to convert R POSIXct vectors to pandas Timestamp vectors was added.

- method :meth:`_repr_html_` for R vectors to display HTML in jupyter.


- Starting several times the singleton :class:`EventProcessor` longer results
  in a :class:`RuntimeError`.

- The target version for the R package `dplyr` mapped is now 0.7.1, and
  :func:`rpy2.robjects.lib.dplyr.src_dt` and
  :func:`rpy2.robjects.lib.dplyr.src_desc` are no longer present.

- :meth:`Environment.keys` is now a iterator to match :meth:`dict.keys`,
  also an interator in Python 3.

- Target version of `ggplot2` library is 2.2.1.

- Option `stringsasfactors` in the constructor for the class `DataFrame`. If `False`, the
  strings are no longer converted to factors. When converting from pandas data frames
  the default is to no longer convert columns of strings to factors.

- The R "magic" for jupyter is now more consistently using the conversion system, and the
  use of custom converters through the magic argument `-c` will work as expected.

- Docker-related files moved to directory docker/ (where variants image for rpy2 are available)

Bugs fixed

- :func:`numpy.float128` is not available on all platforms. The unit test
  for it is now skipped on systems where it is not present

- R pairlist objects can now be sliced.

- Passing parameters names that are empty string to R function was
  causing a segfault.

- Trying to build an atomic R vector from a Python object that has a length,
  but it not a sequence nor an iterator was causing a segfault

Revision 1.41 / (download) - annotate - [select for diffs], Mon Oct 3 12:25:36 2016 UTC (7 years, 1 month ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2017Q3-base, pkgsrc-2017Q3, pkgsrc-2017Q2-base, pkgsrc-2017Q2, pkgsrc-2017Q1-base, pkgsrc-2017Q1, pkgsrc-2016Q4-base, pkgsrc-2016Q4
Changes since 1.40: +2 -2 lines
Diff to previous 1.40 (colored)

Remove some dead code, python-3.3 is no more.

Revision 1.40 / (download) - annotate - [select for diffs], Wed Jun 8 17:43:35 2016 UTC (7 years, 5 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2016Q3-base, pkgsrc-2016Q3, pkgsrc-2016Q2-base, pkgsrc-2016Q2
Changes since 1.39: +2 -2 lines
Diff to previous 1.39 (colored)


Revision 1.39 / (download) - annotate - [select for diffs], Tue Apr 14 11:40:31 2015 UTC (8 years, 7 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2016Q1-base, pkgsrc-2016Q1, pkgsrc-2015Q4-base, pkgsrc-2015Q4, pkgsrc-2015Q3-base, pkgsrc-2015Q3, pkgsrc-2015Q2-base, pkgsrc-2015Q2
Changes since 1.38: +2 -5 lines
Diff to previous 1.38 (colored)

Remove more references to python-2.6.

Revision 1.38 / (download) - annotate - [select for diffs], Mon Apr 13 23:12:42 2015 UTC (8 years, 7 months ago) by rodent
Branch: MAIN
Changes since 1.37: +1 -2 lines
Diff to previous 1.37 (colored)

Removing python26. EOL'd quite some ago and discussed a couple times on
tech-pkg@ and pkgsrc-users@.

Revision 1.37 / (download) - annotate - [select for diffs], Sun Apr 12 10:04:08 2015 UTC (8 years, 7 months ago) by wiz
Branch: MAIN
Changes since 1.36: +4 -2 lines
Diff to previous 1.36 (colored)

Add py-sqlite3 dependency. Fixes last issue from PR 49817.

Revision 1.36 / (download) - annotate - [select for diffs], Fri Apr 10 08:41:42 2015 UTC (8 years, 7 months ago) by wiz
Branch: MAIN
Changes since 1.35: +4 -1 lines
Diff to previous 1.35 (colored)

Fix interpreter path in installed file.

Revision 1.35 / (download) - annotate - [select for diffs], Fri Apr 10 08:36:30 2015 UTC (8 years, 7 months ago) by wiz
Branch: MAIN
Changes since 1.34: +14 -1 lines
Diff to previous 1.34 (colored)

Fix packaging with py33. Disable for py26.

Revision 1.34 / (download) - annotate - [select for diffs], Tue Apr 7 22:14:18 2015 UTC (8 years, 7 months ago) by wiz
Branch: MAIN
Changes since 1.33: +4 -4 lines
Diff to previous 1.33 (colored)

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


- `` 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 ``

- 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.


- The script `` 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


- 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:``
  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

- 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

- ` 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)


- 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

- Missing mapping to ggplot2's `geom_dotplot` function

- Warnings are not longer printed (see Changes below)


- Bumped target version of ggplot2 to

- 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.


- 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)

Revision 1.33 / (download) - annotate - [select for diffs], Tue May 13 17:09:21 2014 UTC (9 years, 6 months ago) by joerg
Branch: MAIN
CVS Tags: pkgsrc-2015Q1-base, pkgsrc-2015Q1, pkgsrc-2014Q4-base, pkgsrc-2014Q4, pkgsrc-2014Q3-base, pkgsrc-2014Q3, pkgsrc-2014Q2-base, pkgsrc-2014Q2
Changes since 1.32: +2 -1 lines
Diff to previous 1.32 (colored)

Requires PCRE.

Revision 1.32 / (download) - annotate - [select for diffs], Wed Feb 26 10:38:07 2014 UTC (9 years, 9 months ago) by wiedi
Branch: MAIN
CVS Tags: pkgsrc-2014Q1-base, pkgsrc-2014Q1
Changes since 1.31: +2 -1 lines
Diff to previous 1.31 (colored)

bulk build suggested readline

Revision 1.31 / (download) - annotate - [select for diffs], Sun Jan 19 22:50:43 2014 UTC (9 years, 10 months ago) by wiz
Branch: MAIN
Changes since 1.30: +4 -6 lines
Diff to previous 1.30 (colored)

Update to 2.3.0:

Release 2.3.0

New Features


- 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


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


- Build dynamic help


- 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.



- :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

- was missing from, 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


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

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

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

- module :mod:`` 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


- :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


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


- 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)



- 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.


- :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)

Revision 1.30 / (download) - annotate - [select for diffs], Tue Sep 11 23:04:32 2012 UTC (11 years, 2 months ago) by asau
Branch: MAIN
CVS Tags: pkgsrc-2013Q4-base, pkgsrc-2013Q4, pkgsrc-2013Q3-base, pkgsrc-2013Q3, pkgsrc-2013Q2-base, pkgsrc-2013Q2, pkgsrc-2013Q1-base, pkgsrc-2013Q1, pkgsrc-2012Q4-base, pkgsrc-2012Q4, pkgsrc-2012Q3-base, pkgsrc-2012Q3
Changes since 1.29: +1 -3 lines
Diff to previous 1.29 (colored)

"user-destdir" is default these days

Revision 1.29 / (download) - annotate - [select for diffs], Wed Sep 14 17:19:18 2011 UTC (12 years, 2 months ago) by hans
Branch: MAIN
CVS Tags: pkgsrc-2012Q2-base, pkgsrc-2012Q2, pkgsrc-2012Q1-base, pkgsrc-2012Q1, pkgsrc-2011Q4-base, pkgsrc-2011Q4, pkgsrc-2011Q3-base, pkgsrc-2011Q3
Changes since 1.28: +3 -1 lines
Diff to previous 1.28 (colored)

Fix build on SunOS.

Revision 1.28 / (download) - annotate - [select for diffs], Wed Jun 29 21:18:08 2011 UTC (12 years, 5 months ago) by alnsn
Branch: MAIN
CVS Tags: pkgsrc-2011Q2-base, pkgsrc-2011Q2
Changes since 1.27: +2 -1 lines
Diff to previous 1.27 (colored)

Add missing LICENSE.


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 (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.

Revision 1.27 / (download) - annotate - [select for diffs], Fri Jul 30 10:36:30 2010 UTC (13 years, 4 months ago) by asau
Branch: MAIN
CVS Tags: pkgsrc-2011Q1-base, pkgsrc-2011Q1, pkgsrc-2010Q4-base, pkgsrc-2010Q4, pkgsrc-2010Q3-base, pkgsrc-2010Q3
Changes since 1.26: +2 -2 lines
Diff to previous 1.26 (colored)

"fortran" -> "fortran77" except where it is clear that it isn't F77.
"fortran" is alias of "fortran77" for now, but it will change later.

Revision 1.26 / (download) - annotate - [select for diffs], Wed Jun 9 21:04:26 2010 UTC (13 years, 5 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2010Q2-base, pkgsrc-2010Q2
Changes since 1.25: +6 -8 lines
Diff to previous 1.25 (colored)

Update py-rpy to 2.1.3

Works with recent R and recent python.

Revision 1.25 / (download) - annotate - [select for diffs], Mon Feb 15 16:32:20 2010 UTC (13 years, 9 months ago) by joerg
Branch: MAIN
CVS Tags: pkgsrc-2010Q1-base, pkgsrc-2010Q1
Changes since 1.24: +3 -1 lines
Diff to previous 1.24 (colored)

Deal with two digit R --version output. Still mark as broken because it
depends on a no-longer existing header.

Revision 1.24 / (download) - annotate - [select for diffs], Fri Sep 19 14:39:00 2008 UTC (15 years, 2 months ago) by joerg
Branch: MAIN
CVS Tags: pkgsrc-2009Q4-base, pkgsrc-2009Q4, pkgsrc-2009Q3-base, pkgsrc-2009Q3, pkgsrc-2009Q2-base, pkgsrc-2009Q2, pkgsrc-2009Q1-base, pkgsrc-2009Q1, pkgsrc-2008Q4-base, pkgsrc-2008Q4, pkgsrc-2008Q3-base, pkgsrc-2008Q3
Changes since 1.23: +2 -2 lines
Diff to previous 1.23 (colored)

Catch up with PLIST changes. Bump revision.

Revision 1.23 / (download) - annotate - [select for diffs], Thu Jun 12 02:14:37 2008 UTC (15 years, 5 months ago) by joerg
Branch: MAIN
CVS Tags: pkgsrc-2008Q2-base, pkgsrc-2008Q2, cwrapper, cube-native-xorg-base, cube-native-xorg
Changes since 1.22: +3 -1 lines
Diff to previous 1.22 (colored)

Add DESTDIR support.

Revision 1.22 / (download) - annotate - [select for diffs], Sat Apr 26 02:41:00 2008 UTC (15 years, 7 months ago) by markd
Branch: MAIN
Changes since 1.21: +3 -3 lines
Diff to previous 1.21 (colored)

Update to match R 2.7.0

Revision 1.21 / (download) - annotate - [select for diffs], Fri Apr 25 20:39:10 2008 UTC (15 years, 7 months ago) by joerg
Branch: MAIN
Changes since 1.20: +1 -2 lines
Diff to previous 1.20 (colored)

- assume that Python 2.4 and 2.5 are compatible and allow checking for
- remove PYTHON_VERSIONS_COMPATIBLE that are obsoleted by the 2.3+
default. Modify the others to deal with the removals.

Revision 1.20 / (download) - annotate - [select for diffs], Wed Nov 7 19:49:36 2007 UTC (16 years ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2008Q1-base, pkgsrc-2008Q1, pkgsrc-2007Q4-base, pkgsrc-2007Q4
Changes since 1.19: +3 -2 lines
Diff to previous 1.19 (colored)

Fix PLIST, bump PKGREVISION for the new R.

Revision 1.19 / (download) - annotate - [select for diffs], Wed Mar 14 11:55:41 2007 UTC (16 years, 8 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2007Q3-base, pkgsrc-2007Q3, pkgsrc-2007Q2-base, pkgsrc-2007Q2, pkgsrc-2007Q1-base, pkgsrc-2007Q1
Changes since 1.18: +3 -4 lines
Diff to previous 1.18 (colored)

Update py-rpy to 0.99.0

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. '' 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
* The 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.

Revision 1.18 / (download) - annotate - [select for diffs], Thu Feb 22 19:26:47 2007 UTC (16 years, 9 months ago) by wiz
Branch: MAIN
Changes since 1.17: +3 -3 lines
Diff to previous 1.17 (colored)

Whitespace cleanup, courtesy of pkglint.
Patch provided by Sergey Svishchev in private mail.

Revision 1.17 / (download) - annotate - [select for diffs], Tue Jun 20 19:54:14 2006 UTC (17 years, 5 months ago) by joerg
Branch: MAIN
CVS Tags: pkgsrc-2006Q4-base, pkgsrc-2006Q4, pkgsrc-2006Q3-base, pkgsrc-2006Q3, pkgsrc-2006Q2-base, pkgsrc-2006Q2
Changes since 1.16: +4 -4 lines
Diff to previous 1.16 (colored)

Catch up with R 2.3.1: different module name, different output of
R --version, different dependency. Bump revision.

Revision 1.16 / (download) - annotate - [select for diffs], Fri Jun 2 23:34:26 2006 UTC (17 years, 6 months ago) by joerg
Branch: MAIN
Changes since 1.15: +2 -1 lines
Diff to previous 1.15 (colored)

py-Numeric exists only for 2.2+.

Revision 1.15 / (download) - annotate - [select for diffs], Thu Apr 6 06:22:22 2006 UTC (17 years, 7 months ago) by reed
Branch: MAIN
Changes since 1.14: +2 -2 lines
Diff to previous 1.14 (colored)

Over 1200 files touched but no revisions bumped :)

RECOMMENDED is removed. It becomes ABI_DEPENDS. becomes becomes

BUILDLINK_DEPENDS does not change.

IGNORE_RECOMMENDED (which defaulted to "no") becomes USE_ABI_DEPENDS
which defaults to "yes".

Added to 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).

Revision 1.14 / (download) - annotate - [select for diffs], Sat Mar 4 21:30:08 2006 UTC (17 years, 9 months ago) by jlam
Branch: MAIN
CVS Tags: pkgsrc-2006Q1-base, pkgsrc-2006Q1
Changes since 1.13: +2 -2 lines
Diff to previous 1.13 (colored)

Point MAINTAINER to in the case where no
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

Revision 1.13 / (download) - annotate - [select for diffs], Sun Feb 5 23:10:03 2006 UTC (17 years, 9 months ago) by joerg
Branch: MAIN
Changes since 1.12: +2 -2 lines
Diff to previous 1.12 (colored)

Recursive revision bump / recommended bump for gettext ABI change.

Revision 1.12 / (download) - annotate - [select for diffs], Fri Jan 27 21:50:41 2006 UTC (17 years, 10 months ago) by markd
Branch: MAIN
Changes since 1.11: +2 -2 lines
Diff to previous 1.11 (colored)

Whoops, I forgot to actually fix the PLIST when I last "fixed" this.  Bump

Revision 1.11 / (download) - annotate - [select for diffs], Wed Jan 4 11:09:44 2006 UTC (17 years, 11 months ago) by markd
Branch: MAIN
Changes since 1.10: +4 -1 lines
Diff to previous 1.10 (colored)

Name of .so file depends on version of R built against so fix PLIST
again and depend on the latest version of R. Bump PKGREVISION.

Revision 1.10 / (download) - annotate - [select for diffs], Fri Oct 21 18:41:14 2005 UTC (18 years, 1 month ago) by drochner
Branch: MAIN
CVS Tags: pkgsrc-2005Q4-base, pkgsrc-2005Q4
Changes since 1.9: +2 -3 lines
Diff to previous 1.9 (colored)

update to 0.4.6
changes: many bugfixes, some improvements in mapping R-Python objects

Revision 1.9 / (download) - annotate - [select for diffs], Mon Apr 11 21:46:31 2005 UTC (18 years, 7 months ago) by tv
Branch: MAIN
CVS Tags: pkgsrc-2005Q3-base, pkgsrc-2005Q3, pkgsrc-2005Q2-base, pkgsrc-2005Q2
Changes since 1.8: +1 -2 lines
Diff to previous 1.8 (colored)

Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.

Revision 1.8 / (download) - annotate - [select for diffs], Sun Nov 21 05:31:03 2004 UTC (19 years ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2005Q1-base, pkgsrc-2005Q1, pkgsrc-2004Q4-base, pkgsrc-2004Q4
Changes since 1.7: +2 -1 lines
Diff to previous 1.7 (colored)

Find new location of  Bump PKGREVISION.
Fixes PR pkg/28371

Revision 1.7 / (download) - annotate - [select for diffs], Thu Jul 22 09:16:03 2004 UTC (19 years, 4 months ago) by recht
Branch: MAIN
CVS Tags: pkgsrc-2004Q3-base, pkgsrc-2004Q3
Changes since 1.6: +2 -2 lines
Diff to previous 1.6 (colored)

add python as category
ok'd a while back at pkgsrcCon by agc and wiz

Revision 1.6 / (download) - annotate - [select for diffs], Tue Apr 27 21:26:09 2004 UTC (19 years, 7 months ago) by snj
Branch: MAIN
CVS Tags: pkgsrc-2004Q2-base, pkgsrc-2004Q2
Changes since 1.5: +4 -4 lines
Diff to previous 1.5 (colored)

Convert to buildlink3.

Revision 1.5 / (download) - annotate - [select for diffs], Thu Dec 4 13:50:33 2003 UTC (20 years ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2004Q1-base, pkgsrc-2004Q1
Changes since 1.4: +4 -4 lines
Diff to previous 1.4 (colored)

Fixed bugs

o There was several memory leaks due to bad management of Python

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.

Revision 1.4 / (download) - annotate - [select for diffs], Sun Sep 14 16:43:51 2003 UTC (20 years, 2 months ago) by recht
Branch: MAIN
CVS Tags: pkgsrc-2003Q4-base, pkgsrc-2003Q4
Changes since 1.3: +2 -2 lines
Diff to previous 1.3 (colored)

hange to also install optimized files for distutils packages.
Inspired by FreeBSD "ports".

Fix the PLISTs accordingly.
Also, while at it, remove now obsolete calls in post-install
targets and insure that is in included before builinlinks of
other Python modules.

Discussed with/ok'ed by drochner@.

Revision 1.3 / (download) - annotate - [select for diffs], Thu Jul 17 21:48:04 2003 UTC (20 years, 4 months ago) by grant
Branch: MAIN
Changes since 1.2: +2 -2 lines
Diff to previous 1.2 (colored)


Revision 1.2 / (download) - annotate - [select for diffs], Mon Jun 2 01:18:24 2003 UTC (20 years, 6 months ago) by jschauma
Branch: MAIN
Changes since 1.1: +2 -2 lines
Diff to previous 1.1 (colored)

Use tech-pkg@ in favor of packages@ as MAINTAINER for orphaned packages.
Should anybody feel like they could be the maintainer for any of thewe packages,
please adjust.

Revision / (download) - annotate - [select for diffs] (vendor branch), Tue Dec 10 12:30:58 2002 UTC (20 years, 11 months ago) by markd
Branch: TNF
CVS Tags: pkgsrc-base, netbsd-1-6-1-base, netbsd-1-6-1
Changes since 1.1: +0 -0 lines
Diff to previous 1.1 (colored)

Initial import of py-rpy-0.3.

Package provided by Kent Polk <> 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.

Revision 1.1 / (download) - annotate - [select for diffs], Tue Dec 10 12:30:58 2002 UTC (20 years, 11 months ago) by markd
Branch: MAIN

Initial revision

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