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 I thought I might be using something out of date, so I ran sem:::bootSem.sem and grabbed the function code.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 On Thursday, October 10, 2013 at 6:38 PM, Eric Green wrote: > 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 > > > On Thursday, October 10, 2013 at 3:01 PM, Eric Green wrote: > > > 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 > > > > > > > > On Wednesday, March 20, 2013 1:43:26 PM UTC-4, John Fox wrote: > > > > > > 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 > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > From: r-help-...@r-project.org (http://r-project.org) <javascript:> > > > > [mailto:r-help-...@r-<javascript:> > > > > project.org (http://project.org)] On Behalf Of pedroabg > > > > Sent: Wednesday, March 20, 2013 1:18 PM > > > > To: r-h...@r-project.org (http://r-project.org) <javascript:> > > > > Subject: Re: [R] Bootstrap (bootSem) causes R to crash > > > > > > > > I think we didn't receive this on the list. > > > > > > > > > > > > > > > > -- > > > > View this message in context: http://r.789695.n4.nabble.com/Bootstrap- > > > > bootSem-causes-R-to-crash-tp4661900p4661944.html > > > > Sent from the R help mailing list archive at Nabble.com > > > > (http://Nabble.com). > > > > > > > > ______________________________________________ > > > > r-h...@r-project.org (http://r-project.org) <javascript:> 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. > > > > > > > > > > > > > ______________________________________________ > > > r-h...@r-project.org (http://r-project.org) <javascript:> 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. > > > > > > > > > ______________________________________________ > > R-help@r-project.org (mailto:R-help@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. > > > > -- > > You received this message because you are subscribed to a topic in the > > Google Groups "R-help-archive" group. > > To unsubscribe from this topic, visit > > https://groups.google.com/d/topic/r-help-archive/yL6Z83z2ZxE/unsubscribe. > > To unsubscribe from this group and all its topics, send an email to > > r-help-archive+unsubscr...@googlegroups.com > > (mailto:r-help-archive+unsubscr...@googlegroups.com). > > To post to this group, send email to r-help-arch...@googlegroups.com > > (mailto:r-help-arch...@googlegroups.com). > > Visit this group at http://groups.google.com/group/r-help-archive. > > For more options, visit https://groups.google.com/groups/opt_out. > > > > > > > > [[alternative HTML version deleted]] ______________________________________________ R-help@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.
