rgenetics & galaxy
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
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
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
-
Ivan Merelli -
Oleksandr Moskalenko -
remy d1