[R] segfault during example(svm)

[Claudia Beleites]

Dear Jürgen,

did you update.packages (checkBuilt = TRUE) ?
I recently had segfaults, too on 64bit linux (with rgl, though) and they 
disappeared only after updating with checkBuilt (including also the packages 
originally installed via Dirk's .deb packages.

HTH,

Claudia



On 02/18/2011 09:32 PM, Juergen Rose wrote:
> Am Freitag, den 18.02.2011, 11:53 -0800 schrieb 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
>
>
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> base
>
> It is working at some of my systems and is failing at the most.
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


-- 
Claudia Beleites
Dipartimento dei Materiali e delle Risorse Naturali
Università degli Studi di Trieste
Via Alfonso Valerio 6/a
I-34127 Trieste

phone: +39 0 40 5 58-37 68
email: cbeleites at units.it