[R] segfault caused by `icfit` in `interval` package

[Uwe Ligges]

On 10.10.2010 19:10, Yuliya Matveyeva wrote:
> On the main site I have only found
> R-2.11.1.tar.gz<http://cran.gis-lab.info/src/base/R-2/R-2.11.1.tar.gz>to
> be the latest release (the latest stable release as far as I
> understand
> it). But unfortunately it doesn't pass the `make check` on my system (that
> is probably the reason why the `emerge` command keeps telling me that my R
> version is up-to-date). May be I should post a separate message  about this
> fact, but I am guessing I shouldn't because making a new release suitable
> for all OS's is probably just a matter of time.
> But before I write to the package maintainer directly could you please tell
> if there might be a non-package-specific reason for a segfault in my case ?


Probably it is the package, but we would need a reproducible example to 
check it.

Uwe Ligges


> Sincerely yours,
> Yuliya Matveyeva.
>
> 2010/10/10 Uwe Ligges<ligges at statistik.tu-dortmund.de>
>
>> Please try with the R-2.12.0 ReleaseCandidate and thwe most recent version
>> of the package (please report its version number!).
>>
>> If it still fails, it may be a good idea to contact the package maintainer
>> of interval first.
>>
>> Uwe Ligges
>>
>>
>>
>>
>> On 10.10.2010 17:33, Yuliya Matveyeva wrote:
>>
>>> Dear R community,
>>>   I am using the R package `interval` in order to perform some modelling
>>> tests of the
>>> NPMLE convergence in the case of censoring. So all I am doing is drawing a
>>> sample
>>> from exponential distribution, making it a censored sample and computing
>>> the
>>> NPMLE of
>>> its distribution function. But when run on Linux Calculate 10.4 the
>>> program
>>> keeps
>>> crashing and reporting a segmentation fault
>>> after the call to the `icfit` function when the sample size gets to 70.
>>> When run on Windows 7 it seems to be fine.
>>> That is why I am totally confused and have decided to ask for help.
>>>
>>> I have attached the code I am running which results in a segmentation
>>> fault
>>> if run on Linux Calculate.
>>> It has the seed set to the value which leads to this error. But it is
>>> important to note
>>> that if the parameters used in the program and the seed are changed it
>>> doesn't
>>> necessarily crash.
>>>
>>> Here is the description of my R version and OS:
>>>
>>>   sessionInfo()
>>>>
>>> R version 2.10.1 (2009-12-14)
>>> i686-pc-linux-gnu
>>>
>>> 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
>>>
>>> After calling `icfit` the program quits with the following output
>>> (I have replaced the output concerning the arguments passed to
>>> initcomputeMLE by
>>> <<<<<   arguments passed to initcomputeMLE>>>>>   so that the description of
>>> the
>>>
>>> output wouldn't be too long):
>>>
>>>   *** caught segfault ***
>>> address 0xc, cause 'memory not mapped'
>>>
>>> Traceback:
>>>   1: .Call("ComputeMLEForR", R, B, max.inner, max.outer, tol)
>>>   2: computeMLE(R, B, max.inner = max.inner, max.outer = max.outer,     tol
>>> =
>>> tol)
>>>   3: initcomputeMLE(<<<<<   arguments passed to initcomputeMLE>>>>>)
>>>   4: do.call(initfit, args = list(L = L, R = R, Lin = Lin, Rin = Rin,     A
>>> =
>>> A))
>>>   5: doTryCatch(return(expr), name, parentenv, handler)
>>>   6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>>>   7: tryCatchList(expr, classes, parentenv, handlers)
>>>   8: tryCatch(expr, error = function(e) {    call<- conditionCall(e)    if
>>> (!is.null(call)) {        if (identical(call[[1L]],
>>> quote(doTryCatch)))             call<- sys.call(-4L)        dcall<-
>>> deparse(call)[1L]        prefix<- paste("Error in", dcall, ": ")
>>> LONG<- 75L        msg<- conditionMessage(e)        sm<- strsplit(msg,
>>> "\n")[[1L]]        w<- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type
>>> = "w")        if (is.na(w))             w<- 14L + nchar(dcall, type =
>>> "b")
>>> + nchar(sm[1L],                 type = "b")        if (w>   LONG)
>>> prefix<- paste(prefix, "\n  ", sep = "")    }    else prefix<- "Error :
>>> "    msg<- paste(prefix, conditionMessage(e), "\n", sep = "")
>>> .Internal(seterrmessage(msg[1L]))    if (!silent&&
>>> identical(getOption("show.error.messages"),         TRUE)) {
>>>   cat(msg,
>>> file = stderr())        .Internal(printDeferredWarnings())    }
>>> invisible(structure(msg, class = "try-error"))})
>>>   9: try(do.call(initfit, args = list(L = L, R = R, Lin = Lin, Rin = Rin,
>>> A = A)))
>>> 10: icfit.default(L = left, R = right)
>>> 11: icfit(L = left, R = right)
>>>
>>> Possible actions:
>>> 1: abort (with core dump, if enabled)
>>> 2: normal R exit
>>> 3: exit R without saving workspace
>>> 4: exit R saving workspace
>>>
>>> I would greatly appreciate any help provided.
>>> Sincerely yours,
>>> Yuliya Matveyeva.
>>>
>>>
>>>
>>> ______________________________________________
>>> R-help at 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.
>>>
>>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at 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.