Not to spoil your fun, but this is getting a bit off-topic for R-help. If you
wish to continue the debugging process in public, I think you should move to
R-devel.
Also, it sounds like the problem is in the glmulti package, so you might want
to involve its maintainer at some point.
-pd
On Aug 10, 2012, at 19:51 , Zhang, Peng wrote:
> Thanks! It is interesting that Windows has pointed the problem to Java.
> So it is probable that how I did my debug led me to the wrong direction.
>
> Since I was unsure how to debug S4 class, I copied the source implement
> R function from glmulti package into my testing program.
>
> The segmentation fault will appear when I step to "neotete =
> terms(as.formula(paste("h~",paste(preds, collapse="*"))))". That is why
> I have asked my initial question on the board.
>
> The more interesting thing is that if I don't run library(glmulti), but
> just the following lines, I won't have problem when I stepped to that
> terms function.
>
> I am totally lost. It is not clear to me how to debug S4 class.
>
> Best,
> Peng
>
> ### beginning
> library(glmulti)
>
> testdata = cbind(Y=rnorm(100), data.frame(matrix(rnorm(100*50), ncol = 50)))
>
> glmulti =
> function(y, xr, data, exclude, name, intercept, marginality , bunch,
> chunk, chunks,
> level, minsize, maxsize, minK, maxK,
> method,crit,confsetsize,popsize,mutrate,
> sexrate,imm, plotty, report, deltaM, deltaB, conseq,
> fitfunction, resumefile, includeobjects, ...) {
> if (missing(data))
> tete = terms(y)
> else
> tete = terms(y, data=data)
> oo = attr(tete,"order")
> dep = as.character(attr(tete,"variables"))[2]
> int = attr(tete,"intercept")
> preds = as.character(attr(tete,"variables"))[-(1:2)]
> if (level==2 && max(oo)>1) {
> # get all possible interactions
> interac = attr(tete,"term.labels")[oo==2]
> neotete = terms(as.formula(paste("h~",paste(preds, collapse="*"))))
> neointerac= attr(neotete,"term.labels")[attr(neotete,"order")==2]
> # get exclusions
> for (i in interac)
> neointerac=neointerac[neointerac!=i]
> # same for main effects
> mama = attr(tete,"term.labels")[oo==1]
> exma = preds
> for (j in mama)
> exma = exma[exma!=j]
> exma = c(exma,neointerac)
> } else {
> preds = attr(tete,"term.labels")[oo==1]
> exma=c(1)
> }
> call = match.call()
> call[[match("y", names(call))]] = dep
> call[[length(names(call))+1]] = preds
> names(call)[length(names(call))] ="xr"
> call[[length(names(call))+1]] = exma
> names(call)[length(names(call))] ="exclude"
>
> if (missing(data)) {
> call[[length(names(call))+1]] = environment(y)
> names(call)[length(names(call))] ="data"
> }
> eval(call)
> }
>
> debug(glmulti)
>
> glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16,
> xr=NULL, data = testdata, level = 2)
> ###end
>
> On 08/10/2012 11:47 AM, Henric (Nilsson) Winell wrote:
>> 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.weyla...@gmail.com>
>>>>> wrote:
>>>>>>
>>>>>> On Aug 9, 2012, at 9:14 PM, David Winsemius <dwinsem...@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
>>>>> **********************************************************
>>>>> Electronic Mail is not secure, may not be read every day, and should
>>>>> not be used for urgent or sensitive issues
>>>>>
>>>>> ______________________________________________
>>>>> R-help@r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide
>>>>> http://www.R-project.org/posting-guide.html
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>
>>>>
>>> **********************************************************
>>> Electronic Mail is not secure, may not be read every day, and should
>>> not be used for urgent or sensitive issues
>>>
>>>
>>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be
> used for urgent or sensitive issues
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd....@cbs.dk Priv: pda...@gmail.com
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