Public | Automated Build

Last pushed: 40 minutes ago
Short Description
Bridge between Python and R
Full Description

This is the source tree or distribution for the rpy2 package.

.. image:: https://img.shields.io/pypi/v/rpy2.svg?style=flat-square
:target: https://pypi.python.org/pypi/rpy2

Installation

pip should work out of the box:

pip install rpy2

The package is known to compile on Linux, MacOSX, and Windows
(provided that developper tools are installed, and you are ready
figure out how by yourself).

Alternatively, there is a Docker image available to try rpy2 out
without concerns about the installation process.

To run the ipython console:

docker run -it --rm -p 8888:8888 rpy2/rpy2:2.8.x ipython

To run jupypter notebook on port 8888:

docker run --rm -p 8888:8888 rpy2/rpy2:2.8.x

More information about Docker images can be found in the
documentation <doc/overview.rst>_.

In case you find yourself with this source without any idea
of what it takes to compile anything on your platform, try first

python setup.py install

If this fails, consider looking for pre-compiled binaries (they are available on Linux Red Hat,
CentOS, Debian, Ubuntu, etc...) or using the matching Docker container.

Note that python setup.py develop will appear to work, but will result in an
installation from the rpy directory here. The namespaces will be
incorrect, so don't do that!

Documentation

Documentation is available either in the source tree (to be built),
or online (on readthedocs).

Testing

The testing machinery uses the new unittest functionality, requiring python 2.7+
(or potentially the backported unittest2 library for older python, but this is
not supported). The test suite can be run (once rpy2 is installed) as follows:

python -m rpy2.tests

By providing an argument, like "-v", you'll get verbose output.

Individual tests can be run as follows:

python -m unittest rpy2.robjects.tests.testVector

Test discovery can be attempted as follows (not that it may not work):

python -m unittest discover rpy2.robjects

Prefer python -m rpy2.tests to run all tests.

License

RPy2 can be used under the terms of the GNU
General Public License Version 2 or later (see the file
gpl-2.0.txt). This is the very same license R itself is released under.

Docker Pull Command
Owner
rpy2
Source Repository

Comments (2)
lgautier
3 days ago

I think that this is because R is installed at the system level (/usr/local) and the default user for the container (not an admin) cannot write into the default install directory. Check the parameter "lib" for the function "install.packages" in the R documentation.

baroque
16 days ago

Hi, when i try to use this version of docker to install library:

import rpy2.robjects as robjects
from rpy2.robjects.packages import importr
utils=importr("utils")
package_name = "xgboost"
utils.install_packages(package_name)

it says: /usr/local/lib/python3.5/dist-packages/rpy2/rinterface/init.py:186: RRuntimeWarning: Error in (function (pkgs, lib, repos = getOption("repos"), contriburl = contrib.url(repos, :
unable to create 'NA'

i've tried with several library, but they all show "unable to create 'NA'"

Can you help on this? thanks :)