[Bioc-devel] edgeR crashes when xlsxjars is loaded

[Dan Tenenbaum]

----- Original Message -----
> From: "Steve Lianoglou" <lianoglou.steve at gene.com>
> To: "Ryan C. Thompson" <rct at thompsonclan.org>
> Cc: bioc-devel at r-project.org
> Sent: Monday, December 16, 2013 10:57:44 AM
> Subject: Re: [Bioc-devel] edgeR crashes when xlsxjars is loaded
> 
> Hi Ryan,
> 
> I ran this code w/ the data you sent, and my system does not crash in
> either case ... perhaps you're barking up the wrong tree?
> 
> sessionInof is below,
> 

It didn't crash for me either. It might be helpful to include your sessionInfo.

Mine is:

> sessionInfo()
R Under development (unstable) (2013-10-12 r64048)
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] splines   stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] locfit_1.5-9.1       xlsxjars_0.5.0       rJava_0.9-5         
[4] edgeR_3.5.22         limma_3.19.12        BiocInstaller_1.13.3

loaded via a namespace (and not attached):
[1] grid_3.1.0      lattice_0.20-24

Dan


> -steve
> 
> sessionInfo()
>  R version 3.0.2 (2013-09-25)
>  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] splines   stats     graphics  grDevices utils     datasets
>   methods   base
> 
>  other attached packages:
>  [1] locfit_1.5-9.1 xlsxjars_0.5.0 rJava_0.9-5    edgeR_3.4.2
> limma_3.18.5   devtools_1.4.1
> 
>  loaded via a namespace (and not attached):
>   [1] compiler_3.0.2  digest_0.6.4    evaluate_0.5.1  grid_3.0.2
> httr_0.2        lattice_0.20-24 memoise_0.1     parallel_3.0.2
> RCurl_1.95-4.1  stringr_0.6.2   tools_3.0.2     whisker_0.3-2
> 
> On Mon, Dec 16, 2013 at 10:45 AM, Ryan C. Thompson
> <rct at thompsonclan.org> wrote:
> > Hello,
> >
> > I have found an issue where having the xlsxjars package loaded
> > kills the
> > entire R session with a segfault when "edgeR::estimateDisp" is
> > called on my
> > dataset. The issue seems to be specific to my data, since a random
> > integer
> > matrix of identical dimension does not trigger the bug. Other than
> > being
> > derived from ChIP-Seq input samples, there is nothing special about
> > my data
> > that I know of.
> >
> > I have prepared a test case with a subset of my data that
> > reproducibly
> > triggers the crash. You can find the data and script to reproduce
> > here:
> >
> > https://www.dropbox.com/sh/e4qbd8txll5vysj/NE8xsa6bxo
> >
> > Thanks,
> >
> > -Ryan
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
> 
> --
> Steve Lianoglou
> Computational Biologist
> Genentech
> 
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