Re: [R] Bootstrap (bootSem) causes R to crash

[pedroabg]

I think we didn't receive this on the list.



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[John Fox]

Dear pedtroabq,

I think that it's impossible to know from the information given why R
crashes when bootSem() is called a second time after it worked the first
time (which is how I interpret the message that you reference). I don't
think that bootSem() is doing anything unusual -- it simply refits the model
to bootstrap samples and uses try() to intercept model-fitting failures on
the bootstrap replications.

Also, although it's not relevant to the problem, it's odd not to store the
object returned by bootSem() in a variable, which is perhaps what the author
of the message means by (2).

bootSem() does use a Tk progress bar, and I suppose that it's possible that
Tcl/Tk for X-Windows or X-Windows itself isn't installed, and that's the
source of the error, but I read (1) as implying that the first call to
bootSem() worked. bootSem() only uses a Tk progress var if tcltk is loaded,
but I don't believe on the Mac that this insures that the tcltk package
actually works. If this is indeed the source of the problem, I should
probably avoid the Tk progress bar under Mac OS X because of the inadequate
support out of the box for the tcltk package on that platform.

Best,
John

-----------------------------------------------
John Fox
Senator McMaster Professor of Social Statistics
Department of Sociology
McMaster University
Hamilton, Ontario, Canada

[Eric Green]

Hi everyone,

I'd like to report a similar experience. When I attempt to run the first
CFA example in bootSem(), specifically the line:

system.time(boot.cnes <- bootSem(sem.cnes, R=100, Cov=hcor, data=CNES))


R crashes and I get a notice about X11. I copied my sessionInfo() below.

Any ideas for a workaround?

Thanks
Eric


R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] polycor_0.7-8 sfsmisc_1.0-23 mvtnorm_0.9-9996 corrgram_1.5
[5] seriation_1.0-11 colorspace_1.2-3 gclus_1.3.1 TSP_1.0-8
[9] cluster_1.14.4 GGally_0.4.4 reshape_0.8.4 plyr_1.8
[13] ggplot2_0.9.3.1 xtable_1.7-1 xlsx_0.5.1 xlsxjars_0.5.0
[17] rJava_0.9-4 nFactors_2.3.3 lattice_0.20-23 boot_1.3-9
[21] sem_3.1-3 matrixcalc_1.0-3 MASS_7.3-29 psych_1.3.10
[25] foreign_0.8-55 knitr_1.5 formatR_0.9

loaded via a namespace (and not attached):
[1] dichromat_2.0-0 digest_0.6.3 evaluate_0.5 gtable_0.1.2

[5] labeling_0.2 munsell_0.4.2 proto_0.3-10
RColorBrewer_1.0-5
[9] reshape2_1.2.2 scales_0.2.3 stringr_0.6.2 tools_3.0.1

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[Eric Green]

Hi,

I solved the crashing issue by removing references to tclck. Here is a gist that shows the edits: https://gist.github.com/ericpgreen/6926595

However, I am getting an error about convergence failures:

Error in bootSem2(sem.cnes, R = 100, Cov = hcor, data = CNES) :
more than 10 consecutive convergence failures


As described in my previous message, I am trying to run the first example in ?semBoot, not my own data. The only difference from the example is that I call the modified bootSem2() function I created by commenting out references to tclck. Increasing max.failures does not seem to help.

I'm not sure what is going on, but I think this example should work fine.

Eric

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[Eric Green]

To close the loop on this, I can report that I solved the convergence issue by updating the original semBoot code. I thought I might be using something out of date, so I ran sem:::bootSem.sem and grabbed the function code.

I updated the gist where I create bootSem2() to stop R from crashing on my mac:
> https://gist.github.com/ericpgreen/6926595