----- Original Message ----- > From: "Steve Lianoglou" <lianoglou.st...@gene.com> > To: "Ryan C. Thompson" <r...@thompsonclan.org> > Cc: bioc-devel@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 > <r...@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@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > -- > Steve Lianoglou > Computational Biologist > Genentech > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
