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 o...@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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