[R] R crashes when loading rgl package before minqa package

[Gaspard Lequeux]

Hej,

On Thu, 30 Sep 2010, Ravi Varadhan wrote:

> I get this on Windows (it does not crash):
>
>> library(minqa)
>> library(rgl)
>> newuoa(initpar, optimft)
> Error in newuoa(initpar, optimft) :
>  non-finite x values not allowed in calfun
> In addition: Warning message:
> In log(x[4]) : NaNs produced

Does it crash when you load first rgl and then only minqa? Like this:

library(rgl)
library(minqa)
newuoa(initpar, optimft)

/Gaspard


> This tells me that you should be constraining your parameter x[4] (may be even x[5]) to be non-negative:
>
> Here is what I get with `bobyqa':
>
>> bobyqa(initpar, optimft, lower=c(-Inf, -Inf, -Inf, 0, 0))
> parameter estimates: -5.311767080681, -3861.89005072333, 979.239647766226, 0.268156271922112, 27.6418856936228
> objective: 1457.20987728737
> number of function evaluations: 78
>>
>
>
> Ravi.
>
> ____________________________________________________________________
>
> Ravi Varadhan, Ph.D.
> Assistant Professor,
> Division of Geriatric Medicine and Gerontology
> School of Medicine
> Johns Hopkins University
>
> Ph. (410) 502-2619
> email: rvaradhan at jhmi.edu
>
>
> ----- Original Message -----
> From: Gaspard Lequeux <Gaspard.Lequeux at biomath.ugent.be>
> Date: Wednesday, September 29, 2010 11:40 am
> Subject: [R] R crashes when loading rgl package before minqa package
> To: r-help at r-project.org
>
>
>>  Hej,
>>
>>  Calling newuoa (from the minqa package) makes R crash when the
>> package rgl is loaded first. This however only on certain selected data.
>>
>>  The data used for testing (saved to 'bugs.R'):
>>
>>
>>  xvals = c(1,2,4,5,7,8,9,10,11,12,14,15,16,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36)
>>
>>  yvals = c(857.7597,975.8624,978.2655,979.3034,965.5919,983.8946,992.2512,992.1178,979.5379,974.4269,968.4113,991.5210,977.3361,985.7800,975.5220,974.6880,973.8102,980.7295,982.0034,984.7993,978.4948,970.4351,969.0718,983.7892,976.3637,980.7833,987.1665,976.6000,975.1332,971.0757,989.4693)
>>
>>  initpar = c(-5.1471384, -3861.8905839, 979.2616002, 0.2572355, 27.5705764)
>>
>>  optimft <- function(x) {
>>    yft = x[2] + (x[3] - x[2])/((1 + exp(x[1] * (log(xvals) - log(x[4]))))^x[5])
>>    return(sum((yvals - yft)^2))
>>  }
>>
>>
>>  Sequence of commands needed to make the bug appear:
>>
>>  <Start R>
>>  source('bugs.R')
>>  library(minqa)
>>  library(rgl)
>>  newuoa(initpar, optimft)
>>   => OK
>>
>>  <Start R>
>>  source('bugs.R')
>>  library(rgl)
>>  library(minqa)
>>  newuoa(initpar, optimft)
>>    => Crash: segfault: address 0x18, cause 'memory not mapped'
>>
>>  I found the bug using the package qpcR, where rgl is loaded when
>> loading qpcR while minqa is only loaded later, when needed.
>>
>>
>>  Running on Debian squeeze 64 bit.
>>  R version: R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu
>>  rgl version: 0.91
>>  minqa version:  1.1.9
>>  Rcpp version: 0.8.6 (loaded by minqa)
>>
>>  Kind regards,
>>
>>  Gaspard Lequeux
>>
>>  ______________________________________________
>>  R-help at r-project.org mailing list
>>
>>  PLEASE do read the posting guide
>>  and provide commented, minimal, self-contained, reproducible code.
>
>