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

[Ravi Varadhan]

No.  It still does not crash in Windows.

> library(rgl)
> library(minqa)
Loading required package: Rcpp
> 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
> 

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: Thursday, September 30, 2010 11:43 am
Subject: Re: [R] R crashes when loading rgl package before minqa package
To: r-help at r-project.org


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