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

[Katharine Mullen]

I also cannot reproduce the crash.

> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] minqa_1.1.9 Rcpp_0.8.6  rgl_0.91

On Thu, 30 Sep 2010, Ravi Varadhan wrote:

> 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.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>