[Bioc-devel] edgeR crashes when xlsxjars is loaded

Ryan C. Thompson rct at thompsonclan.org
Mon Dec 16 23:30:25 CET 2013

By the way, here is my sessionInfo after a successful run of the bug 
script (without loading xlsxjars):

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] splines   grDevices datasets  parallel  graphics  utils     stats
[8] methods   base

other attached packages:
 [1] locfit_1.5-9.1       edgeR_3.4.2          limma_3.18.5
 [4] foreach_1.4.1        plyr_1.8             stringr_0.6.2
 [7] IRanges_1.20.6       BiocGenerics_0.8.0   ggplot2_0.9.3.1
[10] BiocInstaller_1.12.0

loaded via a namespace (and not attached):
 [1] codetools_0.2-8    colorspace_1.2-4   dichromat_2.0-0    
 [5] grid_3.0.2         gtable_0.1.2       iterators_1.0.6    
 [9] lattice_0.20-25    MASS_7.3-29        munsell_0.4.2      
[13] RColorBrewer_1.0-5 reshape2_1.2.2     scales_0.2.3       

On Mon 16 Dec 2013 02:30:34 PM PST, Simon Urbanek wrote:
> On Dec 16, 2013, at 5:20 PM, Ryan <rct at thompsonclan.org> wrote:
>> On Mon Dec 16 14:18:41 2013, Steve Lianoglou wrote:
>>> On Mon, Dec 16, 2013 at 2:03 PM, Ryan <rct at thompsonclan.org> wrote:
>>>> I'm quite sure that it is an interaction between something that xlsxjars
>>>> does and edgeR's C code. The example I gave is a reduction from my actual
>>>> script, and I finally figured out that loading the xlsxjars package is what
>>>> triggers the crash. If I comment out the line that loads xlsxjars, then
>>>> everything runs just fine for me.
>>>> My current solution is to use the parallel package to load and use the xlsx
>>>> package only in subprocesses, so the main R process never uses java.
>>> Out of curiosity, are you saying that if you simply load rJava instead
>>> of xlsxjars in the same place (or perhaps load another package that
>>> depends on rJava), is the crash avoided, too?
>> Yes, that's right, if I load rJava instead of xlsxjars, there is no crash. Perhaps loading rJava does not actually launch a Java subprocess, but loading xlxsjars does?
> JVM is not started until you call
> .jinit()
> so try that ..

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