[R] debug vs regular mode

Zhang, Peng pczhang at med.umich.edu
Fri Aug 10 19:51:17 CEST 2012 

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.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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>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>
>> **********************************************************
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>>
>>
>
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