[pymvpa] problem running LARS (via rpy)

[Yaroslav Halchenko]

I am sorry to give a lame response, but could you try with a big newer
R? I have

In [5]:rpy.RVER
Out[6]:'2091'

In [7]:rpy.RVERSION
Out[8]:'2.9.1'

# !!! this one is wrong ;) see below
In [4]:rpy.__version__
Out[4]:'1.2.1'

LARS is 0.9-7-1cran1 as in the debian package from cran2deb repository

and your little snippet works...

d'oh, rpy.__version__ is not actually version of rpy (surprise!) but of numpy
(enjoy "import *");)

In [12]:rpy.rpy_version
Out[14]:'1.0.3'

btw -- little Python hint, no need for '\' to signal for continuation on
the next line if you are within parenthesis (like among the arguments to the
function, or just a tuple).


On Wed, 26 Aug 2009, Epic John wrote:

>    Hi All,
>    I was really happy to find pymvpa a few days ago. I like some of the
>    dataset/classifier abstractions that are present, and while I haven't
>    explored the entire package yet, I am eager to start using it more.
>    I ran into a problem running LARS, however (which was the original
>    reason I looked into pymvpa.) Part of this might stem from my relative
>    lack of knowledge of R/rpy, but I thought I should ask for some help
>    here.
>    I am doing something really basic:
>    training = Dataset(samples=N.array( N.arange(100),ndmin=2,
>    dtype='float').T,\
>                           labels=[0] * 50 + [1] * 50)
>    lrs = LARS()
>    lrs.train(training)
>    That fails with an rpy exception, which basically tells me there is
>    something wrong with the types. I see we are passing a python ndarray
>    as the 'x' argument of lars, which I am guessing is supposed to be
>    converted
>    to an R matrix behind the scenes. At the end something bad happens when
>    the lars code invokes 'dim(x)'. I am using R 2.7.0, rpy-1.0.3. I have
>    been able to do basic things with rpy, such as plotting, which tells me
>    my rpy/R installation is fine. I have pasted the excetion I get at the
>    end of the email.
>    Does anyone have any idea how to get LARS to work?
>    Thanks
>    EJ
>    C:\Python25\lib\site-packages\mvpa\clfs\base.pyc in train(self,
>    dataset)
>        352
>        353         if dataset.nfeatures > 0:
>    --> 354             result = self._train(dataset)
>        355         else:
>        356             warning("Trying to train on dataset with no
>    features present")
>    C:\Python25\lib\site-packages\mvpa\clfs\lars.pyc in _train(self, data)
>        145
>    intercept=self.__intercept,
>        146
>    trace=self.__trace,
>    --> 147
>    use_Gram=self.__use_Gram)
>        148         else:
>        149             # train with specifying max_steps
>    RPy_RException: Error in rep(1, n) : invalid 'times' argument
>    WARNING: Failure executing file: <mvpa_test.py>

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