# # # > 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

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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/