[Bioc-devel] edgeR crashes when xlsxjars is loaded

Ryan rct at thompsonclan.org
Mon Dec 16 23:20:18 CET 2013

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?

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