Installing rpy and rpy2 on RHEL6

Submitted by John on Wed, 2011-06-08 14:38

I wanted to install rpy and rpy2 on Red Hat Enterprise Linux 6. Here's how I did it. There have been several fixes in the rpy SVN repository that have not shown up in the version downloadable from SourceForge. Hopefully that's been fixed by now, but here's how I installed it by retrieving rpy directly from the repository.

First I made sure that the python-devel package was installed to avoid the error src/RPy.h:63:20: error: Python.h: No such file or directory:

yum install python-devel

Then I installed R and R-devel from EPEL:

rpm -Uvh http://download.fedora.redhat.com/pub/epel/6/x86_64/epel-release-6-5.noarch.rpm
yum install R R-devel

Then I downloaded rpy and extracted it:

curl http://rpy.svn.sourceforge.net/viewvc/rpy/trunk/rpy/?view=tar > rpy.tar.gz
tar xvzf rpy.tar.gz 
cd rpy
python setup.py install

Lo and behold, it imports without error:

python -c "import rpy"

Yay!

Besides R and R-devel, rpy2 requires that the readline-devel package be installed, otherwise installation fails with ./rpy/rinterface/_rinterface.c:79:31: error: readline/readline.h: No such file or directory.

yum install readline-devel

After that, rpy2 installs easily:

curl http://pypi.python.org/packages/source/r/rpy2/rpy2-2.2.0.tar.gz#md5=a42a7f1e6ddb10dc3a1886c2f4309fab > rpy2-2.2.0.tar.gz
tar xvzf rpy2-2.2.0.tar.gz 
cd rpy2-2.2.0
python setup.py install

Topic:

Bioinformatics

Python

RHEL6