Thanks, Simon.  I definitely agree, I ran into quite a few errors but were
helpful for me to figure what's wrong.

I did switch the 2012 MacBook Pro, and the problem was gone.

My actually data is much larger.  But, I did copy paste the error, maybe
that's why?

Mike

On Tue, Dec 18, 2012 at 7:27 PM, Simon Urbanek
<simon.urbanek@r-project.org>wrote:

> Mike,
>
> first, as the error tells you, your "y" is not what svm.fs() requires,
> i.e. it has to be a vector of -1 and 1, so in your code that would be
>
> y <- sample(c(-1,1), 20, replace=TRUE)
>
> Then further penalizedSVM is seriously buggy - the author fails to use
> match.arg() on the arguments, so what happens is that all the defaults are
> invalid and break. The consequence is that the user has to specify all
> defaults explicitly, otherwise the code doesn't work (interestingly the
> author specifies everything in the examples - otherwise it would not pass
> checks at all). For example this seem to sort of work (still with some
> warnings):
>
> model <-
> svm.fs(x,y,"scad","interval",inner.val.method="cv",parms.coding="none",show="final")
>
> Given those trivial mistakes in the code and the fact that it uses print()
> all over the place which is plain wrong, I'd be very careful with relying
> on the penalizedSVM package, so use at your own risk.
>
> Finally, this is not a Mac question, please consider using R-help for such
> queries. (And, no, it has nothing to do with memory usage).
>
> Cheers,
> Simon
>
>
> On Dec 18, 2012, at 6:48 PM, C W wrote:
>
> > Dear list,
> > I am trying to run svm.fs() in package penalizedSVM,
> >
> > x <- matrix(rnorm(100), 20, 5)
> >
> > y <- sample(c(0,10), 20, replace=TRUE)
> >
> > model <- svm.fs(x,y)
> >
> > And I get the following warnings and errors.
> >
> > rror in array(0, c(n, p)) : 'dim' specifies too large an array
> >
> > In addition: There were 16 warnings (use warnings() to see them)
> >
> > There were 50 or more warnings (use warnings() to see the first 50)
> >
> >> warnings()
> >
> > Warning messages:
> >
> > 1: In if (fs.method == "1norm" & inner.val.method == "gacv") stop("gacv
> is
> > not availible for 1norm SVM. Use k fold cv instead.") :
> >
> >  the condition has length > 1 and only the first element will be used
> >
> > 2: In if (grid.search == "interval") { ... :
> >
> >  the condition has length > 1 and only the first element will be used
> >
> > 3: In if ((fs.method %in% c("scad", "1norm")) & is.null(bounds)) { ... :
> >
> >  the condition has length > 1 and only the first element will be used
> >
> > 4: In if (fs.method %in% c("DrHSVM") & is.null(bounds)) { ... :
> >
> >
> > I am guessing this is because of the limit memory?
> >
> > Mike
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> >
>
>

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