[R] nu-SVM crashes in e1071

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Mar 3 15:50:19 CET 2010


On Wed, Mar 3, 2010 at 4:08 AM, Häring, Tim (LWF)
<Tim.Haering at lwf.bayern.de> wrote:
> (...)
>> While you're sending your bug report to David, perhaps you can try the
>> SVM from kernlab.
>> It relies on code from libsvm, too, but ... you never know. It can't
>> hurt to try.
> Hi Steve,
> thanks for that hint.
> I tried ksvm()-function bet get an error message:
> model <- ksvm(soil_unit~., train, type="nu-svc")
> Using automatic sigma estimation (sigest) for RBF or laplace kernel
> Error in votematrix[i, ret < 0] <- votematrix[i, ret < 0] + 1 :
>  NAs are not allowed in subscripted assignments
> But there are no NAs in my dataset. I checked it with
> summary(is.na(train))

All the same, it seems there might be something funky with your data?

Not sure how to help debug further. If you like you send an *.rda file
of your soil_unit data offline and I can try, but otherwise I guess
you're on your own?

What if you remove some of the columns of your matrix? Will this
eventually work?

Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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