[R] segfault during example(svm)

[Peter Ehlers]

On 2011-02-18 11:16, Juergen Rose wrote:
> If do:
>> library("e1071")
>> example(svm)
>
> I get:
>
>
> svm>  data(iris)
>
> svm>  attach(iris)
>
> svm>  ## classification mode
> svm>  # default with factor response:
> svm>  model<- svm(Species ~ ., data = iris)
>
> svm>  # alternatively the traditional interface:
> svm>  x<- subset(iris, select = -Species)
>
> svm>  y<- Species
>
> svm>  model<- svm(x, y)
>
> svm>  print(model)
>
> Call:
> svm.default(x = x, y = y)
>
>
> Parameters:
>     SVM-Type:  C-classification
>   SVM-Kernel:  radial
>         cost:  1
>        gamma:  0.25
>
> Number of Support Vectors:  51
>
>
> svm>  summary(model)
>
> Call:
> svm.default(x = x, y = y)
>
>
> Parameters:
>     SVM-Type:  C-classification
>   SVM-Kernel:  radial
>         cost:  1
>        gamma:  0.25
>
> Number of Support Vectors:  51
>
>   ( 8 22 21 )
>
>
> Number of Classes:  3
>
> Levels:
>   setosa versicolor virginica
>
>
>
>
> svm>  # test with train data
> svm>  pred<- predict(model, x)
>
> svm>  # (same as:)
> svm>  pred<- fitted(model)
>
> svm>  # Check accuracy:
> svm>  table(pred, y)
>              y
> pred         setosa versicolor virginica
>    setosa         50          0         0
>    versicolor      0         48         2
>    virginica       0          2        48
>
> svm>  # compute decision values and probabilities:
> svm>  pred<- predict(model, x, decision.values = TRUE)
>
> svm>  attr(pred, "decision.values")[1:4,]
>    setosa/versicolor setosa/virginica versicolor/virginica
> 1          1.196152         1.091460            0.6705626
> 2          1.064621         1.056332            0.8479934
> 3          1.180842         1.074534            0.6436474
> 4          1.110699         1.053143            0.6778595
>
> svm>  # visualize (classes by color, SV by crosses):
> svm>  plot(cmdscale(dist(iris[,-5])),
> svm+      col = as.integer(iris[,5]),
> svm+      pch = c("o","+")[1:150 %in% model$index + 1])
>
>   *** caught segfault ***
> address (nil), cause 'unknown'
>
> Traceback:
>   1: .Call("La_rs", x, only.values, PACKAGE = "base")
>   2: eigen(-x/2, symmetric = TRUE)
>   3: cmdscale(dist(iris[, -5]))
>   4: plot(cmdscale(dist(iris[, -5])), col = as.integer(iris[, 5]),
> pch = c("o", "+")[1:150 %in% model$index + 1])
>   5: eval.with.vis(expr, envir, enclos)
>   6: eval.with.vis(ei, envir)
>   7: source(tf, local, echo = echo, prompt.echo = paste(prompt.prefix,
> getOption("prompt"), sep = ""), continue.echo = paste(prompt.prefix,
> getOption("continue"), sep = ""), verbose = verbose, max.deparse.length
> = Inf,     encoding = "UTF-8", skip.echo = skips, keep.source = TRUE)
>   8: example(svm)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> ..
>
> I did already "update.packages(), what can I still do.

Works just fine for me. What's your sessionInfo()?
Here's mine:
 > sessionInfo()
R version 2.12.1 Patched (2010-12-27 r53883)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252
[3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] e1071_1.5-24 class_7.3-3

loaded via a namespace (and not attached):
[1] tools_2.12.1


Peter Ehlers

 >
>
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