[R] Error with BRugs 0.53 and 0.71, on Win7 with R 2.12.2 and 2.13.0 (crashes R GUI)

Mon May 30 09:57:55 CEST 2011

On 29.05.2011 23:19, Chris Chapman wrote:
> Uwe -- thank you. No, this occurs on three different machines: two at
> work (a Lenovo laptop running Win7-32, plus an HP workstation running
> Win7-64) ... and I just tried another Compaq desktop machine at home
> running WinXP-32, with the same result.
>
> I agree that this seems highly unusual since the examples are so simple
> and obviously work in general; yet it is also highly replicable for me,
> and I'm at a loss as to what might be the root cause given the different
> machines and Windows versions. FWIW, everything else in my R environment
> (Rgui, Tinn-R, RStudio, ggplot2, various other packages) runs OK.
> OpenBUGS in itself also seems OK albeit in limited tests.
>
> Could there be something in the "handleRes()" error that suggests
> anything to examine (firewall, antivirus, file locations, or some file
> permissions, perhaps? -- although those also vary across my machines,
> esp. from work to home).

The only thing I can say is, yes, perhaps.
Sorry, but I am still unable to reproduce so far.

Uwe

>
> Thanks again,
>
> -- Chris
> --------------------------------------------------
> From: "Uwe Ligges" <ligges at statistik.tu-dortmund.de>
> Sent: Sunday, May 29, 2011 10:07 AM
> To: "Chris Chapman" <cnchapman at msn.com>
> Cc: <r-help at r-project.org>
> Subject: Re: [R] Error with BRugs 0.53 and 0.71, on Win7 with R 2.12.2
> and 2.13.0 (crashes R GUI)
>
>> Sounds like a hardware problem to me, since I do not expereice any
>> problems with the example you gave at first. Is this all on the same
>> hardware?
>>
>> Uwe Ligges
>>
>>
>>
>> On 27.05.2011 18:38, Chris Chapman wrote:
>>> I've run into persistent problems with OpenBUGS crashing when using
>>> BRugs .53 and .71, and am hoping someone has suggestions. There is
>>> obviously something unusual going on in my environment, but I'm at a
>>> loss as to where to begin to try to solve it.
>>>
>>> In a nutshell, what happens is that, as soon as I call "modelCheck()"
>>> in BRugs, it gets an error or crashes ... but only some of the time
>>> (90%< p< 100%). Following are details:
>>>
>>> 1. OpenBUGS 3.0.3 + BRugs 0.531:
>>> It works occasionally, but approximately 90% of the time, I get the
>>> following error from modelCheck():
>>> Error in handleRes(res[[3]]) :
>>>
>>> An OpenBUGS module or procedure was called that did not exist.
>>>
>>>
>>>
>>> The specific code seems not to matter, but here is an example (model
>>> taken from the OpenBUGS tutorial):
>>> modelString =
>>> " model
>>> {
>>> for (i in 1:N) {
>>> r[i] ~ dbin(p[i], n[i])
>>> b[i] ~ dnorm(0, tau)
>>> logit(p[i])<- alpha0 + alpha1 * x1[i] + alpha2 * x2[i]
>>> + alpha12 * x1[i] * x2[i] + b[i]
>>> }
>>> alpha0 ~ dnorm(0, 1.0E-6)
>>> alpha1 ~ dnorm(0, 1.0E-6)
>>> alpha2 ~ dnorm(0, 1.0E-6)
>>> alpha12 ~ dnorm(0, 1.0E-6)
>>> tau ~ dgamma(0.001, 0.001)
>>> sigma<- 1 / sqrt(tau)
>>> }
>>> "
>>> print(modelString)
>>> writeLines(modelString,con="model3.txt")
>>> modelCheck( "model3.txt" )
>>>
>>> Which (usually) produces:
>>>> modelCheck( "model3.txt" )
>>> Error in handleRes(res[[3]]) :
>>> An OpenBUGS module or procedure was called that did not exist.
>>>
>>> I've copied at the end of this message an example from a single R
>>> session that shows how it may work sometimes but not others.
>>>
>>>
>>> 2. OpenBUGS 3.2.1 + BRugs 0.71:
>>>
>>> As above, the model occasionally works, but mostly it crashes R on
>>> the modelCheck() line with the error "R for Windows GUI front-end has
>>> stopped working".
>>>
>>>
>>> I've tried the following combinations to try to get it to work:
>>> A. Win7 32-bit + R 2.13 + BRugs 0.531 from standard CRAN repository
>>> (installed from R)
>>> B. Win7 32-bit + R 2.13 + BRugs 0.71 + OpenBUGS 3.2.1 (package and
>>> EXE from OpenBUGS site)
>>> C. Win7 64-bit [different machine] + R 2.13 (32-bit) + BRugs 0.531
>>> D. Win7 64-bit + R 2.13 (32-bit) + BRugs 0.71 + OpenBugs 3.2.1
>>> E. Win7 32-bit + *R 2.12.2* + BRugs 0.531 from standard CRAN
>>> repository (installed from R)
>>> F. Win7 64-bit + R 2.12.2 (32-bit) + BRugs 0.531
>>> G. Win7 64-bit + R 2.12.2 (32-bit) + BRugs 0.71 + OpenBugs 3.2.1
>>> H. ... and various combinations of removing all R and openbugs
>>> versions, clean installs, and trying again
>>>
>>> In all cases, it occasionally works -- especially on first re-install
>>> of the package -- but then generally gives the "handleRes" error with
>>> BRugs 0.531 or crashes with BRugs 0.71.
>>>
>>> Thanks in advance for any suggestions!
>>>
>>>
>>> === example from a a single R session ===
>>>
>>> R version 2.13.0 (2011-04-13)
>>>
>>> Copyright (C) 2011 The R Foundation for Statistical Computing
>>>
>>> ISBN 3-900051-07-0
>>>
>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>>
>>> You are welcome to redistribute it under certain conditions.
>>>
>>> Type 'license()' or 'licence()' for distribution details.
>>>
>>>
>>> Natural language support but running in an English locale
>>>
>>>
>>> R is a collaborative project with many contributors.
>>>
>>> Type 'contributors()' for more information and
>>>
>>> 'citation()' on how to cite R or R packages in publications.
>>>
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>>
>>> 'help.start()' for an HTML browser interface to help.
>>>
>>> Type 'q()' to quit R.
>>>
>>>
>>> Loading required package: proto
>>>
>>> Loading required package: grid
>>>
>>> Loading required package: reshape
>>>
>>> Loading required package: plyr
>>>
>>>
>>> Attaching package: 'reshape'
>>>
>>>
>>> The following object(s) are masked from 'package:plyr':
>>>
>>>
>>> rename, round_any
>>>
>>>
>>> [Previously saved workspace restored]
>>>
>>>
>>>> install.packages("BRugs")
>>>
>>> Installing package(s) into 'C:/Users/cchap/Documents/R/win-library/2.13'
>>>
>>> (as 'lib' is unspecified)
>>>
>>> --- Please select a CRAN mirror for use in this session ---
>>>
>>> also installing the dependency 'coda'
>>>
>>>
>>> trying URL
>>> 'http://cran.fhcrc.org/bin/windows/contrib/2.13/coda_0.14-4.zip'
>>>
>>> Content type 'application/zip' length 200622 bytes (195 Kb)
>>>
>>> opened URL
>>>
>>> downloaded 195 Kb
>>>
>>>
>>> trying URL
>>> 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.13/BRugs_0.5-3.1.zip'
>>>
>>>
>>> Content type 'application/zip' length 5613828 bytes (5.4 Mb)
>>>
>>> opened URL
>>>
>>> downloaded 5.4 Mb
>>>
>>>
>>> package 'coda' successfully unpacked and MD5 sums checked
>>>
>>> package 'BRugs' successfully unpacked and MD5 sums checked
>>>
>>>
>>> The downloaded packages are in
>>>
>>> C:\Users\cchap\AppData\Local\Temp\RtmpoNcfyf\downloaded_packages
>>>
>>>> library(BRugs)
>>>
>>> Loading required package: coda
>>>
>>> Loading required package: lattice
>>>
>>> Welcome to BRugs running on OpenBUGS version 3.0.3
>>>
>>>> # Specify the model in BUGS language, but save it as a string in R:
>>>
>>>> modelString = "
>>>
>>> + model {
>>>
>>> + for ( i in 1:nFlips ) {
>>>
>>> + y[i] ~ dbern( theta )
>>>
>>> + }
>>>
>>> + theta ~ dunif( priorA , priorB )
>>>
>>> + priorA<- 0.6
>>>
>>> + priorB<- 1.0
>>>
>>> + }
>>>
>>> + " # close quote to end modelString
>>>
>>>>
>>>
>>>> # Write the modelString to a file, using R commands:
>>>
>>>> writeLines(modelString,con="model3.txt")
>>>
>>>> # Use BRugs to send the model.txt file to BUGS, which checks the
>>>> model syntax:
>>>
>>>> modelCheck( "model3.txt" )
>>>
>>> model is syntactically correct
>>>
>>>
>>>
>>>
>>> [ . run the model successfully!! .]
>>>
>>>
>>>
>>>
>>> [ . now change just the prior definition and try to re-run .]
>>>
>>>
>>>
>>>
>>>> modelString = "
>>>
>>> + model {
>>>
>>> + for ( i in 1:nFlips ) {
>>>
>>> + y[i] ~ dbern( theta )
>>>
>>> + }
>>>
>>> + theta ~ dunif( priorA , priorB )
>>>
>>> + priorA<- 0.4
>>>
>>> + priorB<- 0.6
>>>
>>> + }
>>>
>>> + " # close quote to end modelString
>>>
>>>>
>>>
>>>> # Write the modelString to a file, using R commands:
>>>
>>>> writeLines(modelString,con="model3.txt")
>>>
>>>> # Use BRugs to send the model.txt file to BUGS, which checks the
>>>> model syntax:
>>>
>>>> modelCheck( "model3.txt" )
>>>
>>> Error in handleRes(res[[3]]) :
>>>
>>> An OpenBUGS module or procedure was called that did not exist.
>>>
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
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>>