Hello again,
i got this message from the maintainer:
Am Montag, den 30.11.2009, 11:22 +0100 schrieb Heiko Strathmann:
> Ok, i reported it.
> thanks for trying it out again.
>
> Am 30. November 2009 11:06 schrieb Uwe Ligges
> <ligges at statistik.tu-dortmund.de>:
> My apologies, that must have been a copy&paste error and the
> essential argument got lost. I can reproduce it now under
> R-2.10.0 both Windows and Linux.
>
> Please report your findings to the package maintainer who
> might be able to debug this under Linux (probably easier than
> under Windows).
>
> Best,
>
>
> Uwe Ligges
>
>
>
>
>
>
> Heiko Strathmann wrote:
> I tried out the code you wrote, it also works for me,
> but it lacks a
> parameter i use in my code.
>
> The problem (at this computer) seems to be this
> "cross"-parameter of
> ksvm - if I, for example, add the parameter cross=10,
> i get the old
> problem:
>
> library("kernlab")
> load("freeze_workspace.RDATA")
> replicate(10, ksvm(kernel="matrix", kernelMatrix,
> trainingDataYs, type="C-svc", C=2, cross=10))
>
> gets me a frozen R process, CTRL-C does not work
> anymore, and the only thing left is to kill it.
>
> (for cross < 4, the thing still works)
>
> (I also just reinstalled my Ubuntu and R)
>
> Heiko Strathmann
>
>
> Am Sonntag, den 29.11.2009, 19:52 +0100 schrieb Uwe
> Ligges:
> Heiko Strathmann wrote:
> Hello uwe,
> Thanks for trying out.
> the freeze happens after about 10 to
> 20 iterations. Did you try as many?
> I just tried again:
>
> library("kernlab")
> load("freeze_workspace.RDATA")
> replicate(100, ksvm(kernel="matrix",
> kernelMatrix, trainingDataYs, type="C-svc",
> C=2))
>
> and everything is still fine (same on Linux).
>
> Uwe Ligges
>
>
>
> Am Sonntag, den 29.11.2009, 17:22
> +0100 schrieb Uwe Ligges:
> I just tried
>
> ksvm(kernel="matrix",
> kernelMatrix, trainingDataYs,
> type="C-svc", cross=10, C=2)
>
> several times on both
> workspaces and both returned
> some results after a couple of
> seconds under the same
> versions (R version 2.10.0 and
> kernlab 0.9-9.) under Windows
> XP.
>
> There mist be something else
> going on...
>
> Best wishes,
> Uwe Ligges
>
>
>
>
>
> Heiko Strathmann wrote:
> Hello again,
>
> the freeze seems to
> depend on the kernel
> matrix.
> With another kernel
> matrix of similiar
> size, gernerated with
> the same
> kernel, but on another
> dataset, there is no
> freeze.
>
> I have put a workspace
> with the working
> matrix and one with
> the freezing
> matrix online for
> testing (see old
> email)
> http://www-stud.uni-due.de/~sfhestra/
>
> In my eyes this
> behavior is really
> strange, and i have no
> clue, what to
> do to solve this.
>
> Regards,
> Heiko Strathmann
>
> Am Sonntag, den
> 29.11.2009, 14:21
> +0100 schrieb Heiko
> Strathmann:
> Hello,
>
> I am using
> kernlab to do
> some binary
> classification
> on aminoacid
> strings.
>
> I am using a
> custom kernel,
> so i use the
> kernel="matrix" option of the
> ksvm method.
>
> My
> (normalized)
> kernel matrix
> is of size
> 1309*1309, my
> results vector
> has the same
> length.
>
> I am using
> C-svc.
>
> My kernlab
> call is
> something
> similiar to
> this:
>
> ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc",
> cross=10, C=2)
>
> To this point,
> everything
> works fine.
>
> But now, i
> want to do a
> search for a
> good C
> Parameter, so
> I call the
> ksvm method
> multiple times
> in a loop,
> with changing
> parameters.
> This loop
> freezes after
> a few
> iterations.
>
>
> The following
> simple example
> also freezes
> after few
> iterations
> (the
> number
> varies). See
> that the ksvm
> call is always
> the same in
> every
> iteration:
>
> for (i in
> c(1:20)) {
>
> print(i)
>
> ksvm(kernel="matrix", kernelMatrix, trainingDataYs,
> type="C-svc",
> cross=10, C=2)
> }
>
>
> Does anybody
> have an idea
> what causes
> this? I am new
> to R and
> kernlab,
> perhaps i
> missed
> something?
>
> I put my
> workspace
> online, which
> contains the
> kernel matrix
> and the
> training
> labels. Simply
> load
> workspace,
> kernlab
> library and
> paste the
> example code
> to reproduce:
> http://www-stud.uni-due.de/~sfhestra/
>
> I am using R
> version 2.10.0
> and kernlab
> 0.9-9.
>
> Thanks for
> your help!
>
> Regards,
> Heiko
> Strathmann
>
>
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