FWIW, the solution I have for now is to use dump(ls(), file="") to get a
deparsed string representation of all the objects in memory, which can
then be pickled. I'm not having problems with it right now in any simple
cases, but I can imagine there are situations where deparsing gets
hairy, so being able to pickle the R globalEnv or somehow being able to
route the file output of R's save.image command to a python object that
can then be pickled would be the best....
Cheers,
-brandon invergo
On Thu, 2009-04-30 at 01:01 +0200, Brandon Invergo wrote:
> I'm trying to do something similar: I'd like to create a save file that
> includes the current state of the R environment. I don't want to create
> a separate file for the R environment via one of R's built-in commands,
> so I thought I'd pickle globalEnv alongside some other objects I'm
> pickling. When I try to pickle the globalEnv, I get this error:
> cPickle.PicklingError: Can't pickle <type 'rinterface.SexpEnvironment'>:
> import of module rinterface failed
>
>
> How have other people gone about storing their R objects?
>
> Thanks!
> brandon invergo
>
>
>
> On Mon, 2009-04-06 at 11:29 -0400, Réjean Ducharme wrote:
> > Hi all,
>
> I'm using Rpy2 to train a logistic regressor (using the "glm" function
> in R), and I need to save the model for futher use.
> I naively try to use pickle, but I have an error message:
>
> import rpy2.robjects as robjects
> fit = robjects.r.glm(formula=f, family=robjects.r.binomial(), data=data)
> output = open('glm.pickle', 'w')
> pickle.dump(fit, output)
>
> >>> pickle.PicklingError: Can't pickle <type
> 'rinterface.SexpVector'>:
> it's not found as rinterface.SexpVector
>
>
> Is there another way to save a Rpy2 object???
>
> Thanks,
> Rejean Ducharme
>
>
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