[R] kernlab's ksvm method freeze

[Uwe Ligges]

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
>>>>>>
>>>>>>
>>>>> ______________________________________________
>>>>> R-help at 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.
>>>
> 
>