[R] debug vs regular mode

[Henric (Nilsson) Winell]

On 2012-08-10 15:42, Zhang, Peng wrote:

> You are right. I am running Arch Linux. However, I obtained a
> segmentation directly, so didn't know where to find the bug??
>
>   >  library("glmulti")
> Loading required package: rJava
>   > testdata = cbind(Y=rnorm(100), data.frame(matrix(rnorm(100*50), ncol
> = 50)))
>   > glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16,
> data= testdata, level = 2)
> Segmentation fault
>
> Is this information "Error in .jnew("glmulti/ModelGenerator", y,
> jarray(xc), .jarray(xq),  : java.lang.ArrayIndexOutOfBoundsException:
> 15" only in Windows, or did you see it under Fedora as well?

Windows only.  Fedora just returned "Segmentation fault".


//Henric



>
> Thank you!
>
> Peng
>
> BTW:
>
> $ uname -a
> Linux Precision 3.4.7-1-ARCH #1 SMP PREEMPT Sun Jul 29 22:02:56 CEST
> 2012 x86_64 GNU/Linux
>
>   > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>    [7] LC_PAPER=C                 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
>
>
> On 08/10/2012 09:25 AM, Henric (Nilsson) Winell wrote:
>> On 2012-08-10 06:10, Zhang, Peng wrote:
>>
>>> Thanks to both for your reply.
>>>
>>> library(glmulti)
>>> testdata = cbind(Y=rnorm(100), data.frame(matrix(rnorm(100*50), ncol
>>> = 50)))
>>> glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16, data
>>> = testdata, level = 2)
>>>
>>> This is reproducible to get a segmentation fault.
>>
>> There's some information missing here, notably the output from
>> 'sessionInfo()', but I guess this is under GNU/Linux.  I can confirm a
>> seg. fault under Fedora FC17 x86_64.
>>
>> Under Windows 7 64-bit, however, we get some further info:
>>
>>> library("glmulti")
>> Loading required package: rJava
>>> testdata = cbind(Y=rnorm(100), data.frame(matrix(rnorm(100*50), ncol
>> = 50)))
>>> glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16,
>> data
>> + = testdata, level = 2)
>> Initialization...
>> Error in .jnew("glmulti/ModelGenerator", y, .jarray(xc), .jarray(xq),  :
>>    java.lang.ArrayIndexOutOfBoundsException: 15
>>>
>>> sessionInfo()
>> R version 2.15.1 Patched (2012-08-06 r60178)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252
>> [3] LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C
>> [5] LC_TIME=Swedish_Sweden.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods base
>>
>> other attached packages:
>> [1] glmulti_1.0.4 rJava_0.9-3
>>>
>>
>> So, this doesn't seem to be a bug in R and is thus likely to need the
>> attention of the 'glmulti' package's maintainer.
>>
>>
>> HTH,
>> Henric
>>
>>
>>
>>> But I have troubles to
>>> extract the exact information from this S4 class to make a simpler
>>> example because of my limited knowledge on S4 class. The author of the
>>> package is busy at the moment, and does not have time to look into it.
>>>
>>> Peng
>>>
>>> On 08/09/2012 10:25 PM, R. Michael Weylandt <michael.weylandt at gmail.com>
>>> wrote:
>>>>
>>>> On Aug 9, 2012, at 9:14 PM, David Winsemius <dwinsemius at comcast.net>
>>>> wrote:
>>>>
>>>>> On Aug 9, 2012, at 4:56 PM, Zhang, Peng wrote:
>>>>>
>>>>>> Dear all,
>>>>>>
>>>>>> I had a R segmentation fault, and then invoked debug mode and ran
>>>>>> step
>>>>>> by step.
>>>>>
>>>>>> 2. Why does the same function behave differently under debug and
>>>>>> regular
>>>>>> mode?
>>>>> I cannot help you there.
>>>>>
>>>> Though a reproducible segfault is certainly worth a bug report if
>>>> you can do so, in debug or regular modes.
>>>>
>>>> You may wish to search stackoverflow for tips on how to make a great
>>>> reproducible example in R.
>>>>
>>>> Michael
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>>
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