kernlab's ksvm method freeze

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