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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