Hi,

For information, here is my install script for rpy, because I had to reinstall all of that on CentOS 5.4... :

#!/bin/bash

#

#

#

...

echo "< RPY for R and Python **********************************"

cd rpy;

export

...

LD_LIBRARY_PATH=/opt/gridengine/lib/lx26-amd64:/lib64:/usr/lib64:/usr/local/lib64:/usr/lib/:/usr/local/lib/

#export R_HOME=/usr/lib64/R/

...

# remy modifications 17/01/2012

unset R_HOME

...

export RHOME=/usr/lib64/R/

...

cp -s /usr/lib64/R/lib/* /usr/lib64/R/bin/

...

# rajout 17/01/2012

mkdir -p /usr/share/R/include

...

cp -s /usr/lib64/R/include/* /usr/share/R/include/

cp -s /usr/lib64/R/include/* /usr/local/include/

cp -s /usr/lib64/R/include/* /usr/include/

cp -s /usr/lib64/R/lib/* /usr/lib/

cp -s /usr/lib64/R/lib/* /lib64/

cp -s /usr/lib64/R/lib/* /usr/local/lib64/

cp -s /usr/lib64/R/lib/* /usr/local/lib/

...

ldconfig

...

cd trunk/rpy

...

sed -i "s/libraries=['R']/libraries=['R','Rlapack']/g" setup.py

# added 17/01/2012

sed -i "s|/usr/share/R/include|/usr/lib64/R/include/|g" setup.py

# added 17/01/2012

sed -i 's|[0-9]+\.[0-9]+\.[0-9]+|[0-9].[0-9]+.[0-9]|g'

...

rpy_tools.py

...

python setup.py install

If it does not work, try with R_HOME.

2011/11/25 Oleksandr Moskalenko om@hpc.ufl.edu

On Nov 25, 2011, at 6:52 AM, Ivan Merelli wrote:

Hi,

I'm trying to use rgenetics in galaxy, but I have some problem in installting rpy-1.0.3 with R-2.13.1.

I found this guide, which is about the same problem of mine: http://gmod.827538.n3.nabble.com/Rpy-1-0-3-and-R-2-13-1-td3359590.html

but didn't work for me (although the part about the modulefile is quite obscure for me). The problem seems to be correlated to an header file (Rdevices.h) which is no more present in the latest R distribution.

Any hints to solve this problem? May I use rpy2?

Best, Ivan

---

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There is information on solving this available via a web search - http://www.mail-archive.com/rpy-list@lists.sourceforge.net/msg01500.html for instance. In short,

• Unpack rpy-1.0.3 and patch the following files:
• rpm_tools.py

version = re.search(" +([0-9].[0-9]+.[0-9])", output)

• setup.py

include_dirs = [ os.path.join(RHOME.strip(), 'include'), 'src', '/usr/share/R/include', '/apps/R/2.13.1/include' ]

• Build rpy with

python setup.py install

Cheers,

Alex

---

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