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

___________________________________________________________
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:

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

Reply via email to