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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