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

[Ravi Varadhan]

You data is not good enough for the model that you are trying to fit (or conversely, the model is not appropriate for the data).  

Some of the parameters in your model will not be estimable because there is no information in the data.

See the following:

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)

fn <- function(x) {
yft = x[2] + (x[3] - x[2])/((1 + exp(x[1] * (log(xvals) - log(x[4]))))^x[5])
return(yft)
}

plot(xvals, yvals, type="p")
lines(xvals, fn(initpar))

Hope this helps,
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: Ravi Varadhan <rvaradhan at jhmi.edu>
Date: Thursday, September 30, 2010 10:15 am
Subject: Re: [R] R crashes when loading rgl package before minqa package
To: Gaspard Lequeux <Gaspard.Lequeux at biomath.ugent.be>
Cc: r-help at r-project.org


> 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
>  >
>  
>  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.
>  
>  ______________________________________________
>  R-help at r-project.org mailing list
>  
>  PLEASE do read the posting guide 
>  and provide commented, minimal, self-contained, reproducible code.