Ok, i reported it.
thanks for trying it out again.

Am 30. November 2009 11:06 schrieb Uwe Ligges <
ligges@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/<http://www-stud.uni-due.de/%7Esfhestra/>
>>>>>>
>>>>>> 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/<http://www-stud.uni-due.de/%7Esfhestra/>
>>>>>>>
>>>>>>> I am using R version 2.10.0 and kernlab 0.9-9.
>>>>>>>
>>>>>>> Thanks for your help!
>>>>>>>
>>>>>>> Regards,
>>>>>>> Heiko Strathmann
>>>>>>>
>>>>>>>
>>>>>>>  ______________________________________________
>>>>>> R-help@r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>> PLEASE do read the posting guide
>>>>>> http://www.R-project.org/posting-guide.html
>>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>>
>>>>>
>>>>
>>
>>

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