[pymvpa] RPy and ENET

[Michael Hanke]

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
>



Michael


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