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: rvarad...@jhmi.edu
----- Original Message -----
From: Gaspard Lequeux <gaspard.lequ...@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@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: 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.
> >
> >
>
> ______________________________________________
> 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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