[Bioc-devel] edgeR crashes when xlsxjars is loaded
Steve Lianoglou
lianoglou.steve at gene.com
Mon Dec 16 19:57:44 CET 2013
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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> 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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