R help - Mar 2011 - *** caught segfault *** when using impute.knn (impute package)

hi,

i am getting an error when calling the impute.knn
function (see the screenshot below).
what is the problem here and how can it be solved?


screenshot:

##################
  *** caught segfault ***
address 0x513c7b84, cause 'memory not mapped'

Traceback:
  1: .Fortran("knnimp", x, ximp = x, p, n, imiss = imiss, irmiss, 
as.integer(k), double(p), double(n), integer(p), integer(n),     PACKAGE 
= "impute")
  2: knnimp.internal(x, k, imiss, irmiss, p, n, maxp = maxp)
  3: knnimp(x, k, maxmiss = rowmax, maxp = maxp)
  4: impute.knn(dummy0, k)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

##################

thanks for your help in advance!

tina

-- 

Bettina Kulle Andreassen

University of Oslo

Department of Biostatistics

and

Institute for Epi-Gen (Faculty Division Ahus)

tel:
+47 22851193
+47 67963923

On 02.03.2011 15:31, Bettina Kulle Andreassen wrote:
> hi,
>
> i am getting an error when calling the impute.knn
> function (see the screenshot below).
> what is the problem here and how can it be solved?
Please write to the package maintainers. This is probably a bug in the 
package.

Uwe Ligges

>
>
> screenshot:
>
> ##################
> *** caught segfault ***
> address 0x513c7b84, cause 'memory not mapped'
>
> Traceback:
> 1: .Fortran("knnimp", x, ximp = x, p, n, imiss = imiss, irmiss,
> as.integer(k), double(p), double(n), integer(p), integer(n), PACKAGE >
"impute")
> 2: knnimp.internal(x, k, imiss, irmiss, p, n, maxp = maxp)
> 3: knnimp(x, k, maxmiss = rowmax, maxp = maxp)
> 4: impute.knn(dummy0, k)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
> ##################
>
> thanks for your help in advance!
>
> tina
>

On Wed, Mar 2, 2011 at 6:31 AM, Bettina Kulle Andreassen
<b.k.andreassen at medisin.uio.no> wrote:
> hi,
>
> i am getting an error when calling the impute.knn
> function (see the screenshot below).
> what is the problem here and how can it be solved?
>
>
> screenshot:
>
> ##################
> ?*** caught segfault ***
> address 0x513c7b84, cause 'memory not mapped'
>
> Traceback:
> ?1: .Fortran("knnimp", x, ximp = x, p, n, imiss = imiss, irmiss,
> as.integer(k), double(p), double(n), integer(p), integer(n), ? ? PACKAGE
> "impute")
> ?2: knnimp.internal(x, k, imiss, irmiss, p, n, maxp = maxp)
> ?3: knnimp(x, k, maxmiss = rowmax, maxp = maxp)
> ?4: impute.knn(dummy0, k)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
> ##################
>
> thanks for your help in advance!
>
I've been seeing the same problem for some time. It tends to happen
when one of the clusters the function splits the data into has the
same size as k. Make sure k is smaller than your data size, too. Try
moving k a little bit, for example set k=9 or k=11 (the default is 10)
and see if the crash goes away. I am CCing the package maintainer.

HTH,

Peter
> Bettina Kulle Andreassen
>
> University of Oslo
>
> Department of Biostatistics
>
> and
>
> Institute for Epi-Gen (Faculty Division Ahus)
>
> tel:
> +47 22851193
> +47 67963923
>
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