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: rvarad...@jhmi.edu
>
>
>----- Original Message -----
>From: Gaspard Lequeux <gaspard.lequ...@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@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@r-project.org mailing list
>>
>> PLEASE do read the posting guide
>> and provide commented, minimal, self-contained, reproducible code.
>
>
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