Build R with the following additions:
- Configuration:

Edit the config.site file and add the

CFLAGS= -g -02 -fPIC

Run:

./configure  --prefix=/apps/R/2.13.1 --enable-R-shlib

Run:

make; make install

Copy the 'include' directory to /apps/R/2.13.1
Write and load the modulefile
Load the python/2.6.5 modulefile Galaxy uses.
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

On Sep 22, 2011, at 3:38 PM, Oleksandr Moskalenko wrote:

On Sep 22, 2011, at 1:56 PM, Assaf Gordon wrote:

Hello,

It seems this issue (rpy) pops up every now and then:
Has anyone managed to get rpy-1.0.3 working properly with R-13.1 (including loading packages) ?

I already replied to Assaf, so this is a list copy. Yes, this combination works. I recently installed R and Rpy for the local Galaxy instance I'm building. I use modules (lmod) to set up the environment.

# python
Python 2.6.5 (r265:79063, Jul 22 2010, 17:49:40)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-44)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
import rpy
rpy.r.version["version.string"]
'R version 2.13.1 (2011-07-08)'
[ name for name in rpy.r.library()["results"] if name[0] == "limma" ]
[['lrpy.r.version["version.string"]library', 'Linear Models for Microarray Data']]

Cheers,

Alex

After compiling R-2.13.1 from source, and recompiling rpy-1.0.3, I get the following error when trying to load an R module through rpy:
===================
$ python
import rpy
rpy.r.version["version.string"]
'R version 2.13.1 (2011-07-08)'

### Make sure the "limma" library is installed:
[ name for name in rpy.r.library()["results"] if name[0] == "limma" ]
[['limma', '/usr/local/lib64/R/library', 'Linear Models for Microarray Data']]

### Trying to load 'limma' fails, with unspecified error:
rpy.r.library("limma")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
rpy.RPy_RException: Error: package/namespace load failed for 'limma'
======================

I've checked that:
1. The "limma" library is definitely installed and loads properly from R.
2. Some libraries can be loaded from RPY (e.g. "stats", "tcltk", and others)
3. Many bioconductor libraries can't be loaded from RPY (but all load properly from R).
4. All of the above used to work in R-2.11.1

Any ideas ?

Thanks,
-gordon

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___________________________________________________________
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

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