... and you could also see if you have any better luck with another SVM
package like kernlab, perhaps

On Thursday, March 15, 2012, Sean Davis <sdavis2@mail.nih.gov> wrote:
> Hi, Javier.
>
> Your problem is not really related to bioconductor.  I'd suggest you
> email the e1071 maintainer.
>
> Sean
>
>
> 2012/3/15 Javier Pérez Florido <jpflorido@gmail.com>:
>> Dear list,
>> For R version 2.13.0, I had no problems running the following code (CMA
>> package was used to load golub data, but detach afterwards trying to
isolate
>> the problem):
>>
>> library(CMA)
>> data(golub)
>> detach(package:CMA)
>> library(e1071)
>>
>> golubY <- golub[,1]
>> golubX <- as.matrix(golub[,-1])
>> ratio <- 2/3
>> golubY2 <- as.factor(golubY)
>> levels(golubY2) <- 1:nlevels(golubY2)
>> golubY2<-as.numeric(golubY2)-1
>>
>> set.seed(777)
>> learnind <- sample(length(golubY), size=floor(ratio*length(golubY)))
>>
>> Xtrain=golubX[learnind,]
>> Ytrain=as.factor(golubY2[learnind])
>>
>> svm.model <-
>>
svm(x=Xtrain,y=Ytrain,seed=set.seed(321),cost=1,kernel="linear",type="C-classification")
>>
>> However, for R version 2.14.2 and running the same code, R was closed by
>> Windows because a problem in svm function. Here is the session info:
>>
>> R version 2.14.2 (2012-02-29)
>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252
>> [3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
>> [5] LC_TIME=Spanish_Spain.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] e1071_1.6      class_7.3-3    Biobase_2.14.0
>>
>> loaded via a namespace (and not attached):
>> [1] CMA_1.12.0   tools_2.14.2
>>
>> %%%%%%%%%%%%%%
>>
>> I've tried in Linux O.S. too, obtaining the following error:
>>
>>
>>  *** caught segfault ***
>> address (nil), cause 'memory not mapped'
>>
>> Traceback:
>>  1: .C("svmtrain", as.double(if (sparse) x@ra else t(x)), as.integer(nr),
>>   as
>> .integer(ncol(x)), as.double(y), as.integer(if (sparse) x@ia else 0),
>> as.int
>> eger(if (sparse) x@ja else 0), as.integer(type), as.integer(kernel),
>> as.inte
>> ger(degree), as.double(gamma), as.double(coef0), as.double(cost),
>> as.double(
>> nu), as.integer(weightlabels), as.double(class.weights),
>> as.integer(length(c
>> lass.weights)), as.double(cachesize),     as.double(tolerance),
>> as.double(epsilo
>> n), as.integer(shrinking),     as.integer(cross), as.integer(sparse),
>> as.integer
>> (probability),     as.integer(seed), nclasses = integer(1), nr =
integer(1),
>>  index = integer(nr), labels = integer(nclass), nSV = integer(nclass),
>> rho =
>>  double(nclass * (nclass - 1)/2), coefs = double(nr *         (nclass -
1)),
>> sig
>> ma = double(1), probA = double(nclass *         (nclass - 1)/2), probB =
>> double(
>> nclass * (nclass - 1)/2),     cresults = double(cross), ctotal1 =
double(1),
>> cto
>> tal2 = double(1),     error = err, PACKAGE = "e1071")
>>  2: svm.default(x = Xtrain, y = Ytrain, seed = set.seed(321), cost = 1,
>> kern
>> el = "linear", type = "C-classification")
>>  3: svm(x = Xtrain, y = Ytrain, seed = set.seed(321), cost = 1, kernel =
>> "linear
>> ",     type = "C-classification")
>>
>> Possible actions:
>> 1: abort (with core dump, if enabled)
>> 2: normal R exit
>> 3: exit R without saving workspace
>> 4: exit R saving workspace
>> Selection:
>>
>> R version 2.14.2 (2012-02-29)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>>  [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
>>  [7] LC_PAPER=C                     LC_NAME=C
>>  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] e1071_1.6

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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