[Bioc-devel] edgeR crashes when xlsxjars is loaded

Ryan C. Thompson rct at thompsonclan.org
Mon Dec 16 23:34:18 CET 2013

Indeed, loading rJava and calling .jinit() also triggers the bug. I 
have updated my script (same URL as before) to demonstrate this. I run 
the bad code before and after calling .jinit(), and it only crashes the 
second time.

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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