[Bioc-devel] edgeR crashes when xlsxjars is loaded

[Steve Lianoglou]

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,

-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
>
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-- 
Steve Lianoglou
Computational Biologist
Genentech