Just for reference in case anyone runs into this problem here is my personal
installation log:
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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and other Galaxy lists, please use the interface at:
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and other Galaxy lists, please use the interface at:
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