[pymvpa] RPy and ENET

[Per B. Sederberg]

On Mon, Jan 11, 2010 at 7:12 AM, Michael Hanke <michael.hanke at gmail.com> wrote:
> On Sun, Jan 10, 2010 at 07:49:20AM -0500, Per B. Sederberg wrote:
>> Hi Everyone:
>>
>> I've committed an updated GLMNET to my per/master branch, along with
>> some tests.  It seems to be working on my end.
>
> I merged and tried running the unittest for GLMNET. However I get:
>
> ERROR: Failure: RRuntimeError (Error in function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
>  no library trees found in 'lib.loc'
> )
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "/usr/lib/pymodules/python2.5/nose/loader.py", line 379, in loadTestsFromName
>    addr.filename, addr.module)
>  File "/usr/lib/pymodules/python2.5/nose/importer.py", line 39, in importFromPath
>    return self.importFromDir(dir_path, fqname)
>  File "/usr/lib/pymodules/python2.5/nose/importer.py", line 86, in importFromDir
>    mod = load_module(part_fqname, fh, filename, desc)
>  File "/home/michael/hacking/pymvpa.dev/mvpa/tests/test_glmnet.py", line 12, in <module>
>    from mvpa.clfs.glmnet import GLMNET_R,GLMNET_C
>  File "/home/michael/hacking/pymvpa.dev/mvpa/clfs/glmnet.py", line 20, in <module>
>    externals.exists('glmnet', raiseException=True):
>  File "/home/michael/hacking/pymvpa.dev/mvpa/base/externals.py", line 452, in exists
>    exec _KNOWN[dep]
>  File "<string>", line 1, in <module>
>  File "/usr/lib/python2.5/site-packages/rpy2/robjects/__init__.py", line 423, in __call__
>    res = super(RFunction, self).__call__(*new_args, **new_kwargs)
> RRuntimeError: Error in function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  :
>  no library trees found in 'lib.loc'
>
>
> The externals test for GLMNET fails, although I can do:
>
> michael at meiner:(git)~/hacking/pymvpa.dev:[mh/master]$ R
>
> R version 2.10.0 (2009-10-26)
> Copyright (C) 2009 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
>> library(glmnet)
> Loading required package: Matrix
> Loading required package: lattice
>>
>
>

Hmmmmm.  What happens when you do the following in ipython:

import rpy2.robjects
rpy2.robjects.r.library('glmnet')

P

>
> Michael
>
>
> --
> GPG key:  1024D/3144BE0F Michael Hanke
> http://mih.voxindeserto.de
>
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