[BioC] problems using the latest version of e1071 (svm)

[Sean Davis]

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 at 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 at ra else t(x)), as.integer(nr),
>   as
> .integer(ncol(x)), as.double(y), as.integer(if (sparse) x at ia else 0),
> as.int
> eger(if (sparse) x at 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      class_7.3-3    Biobase_2.14.0
>
> loaded via a namespace (and not attached):
> [1] CMA_1.12.0   tools_2.14.2
>
> Thanks,
> Javier
>
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