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) ?
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:
>>> import rpy
'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 == "limma" ]
[['limma', '/usr/local/lib64/R/library', 'Linear Models for Microarray Data']]
### Trying to load 'limma' fails, with unspecified error:
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
4. All of the above used to work in R-2.11.1
Any ideas ?
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: