[Bioc-devel] segfault in csaw native code

Aaron Lun alun at wehi.edu.au
Wed Mar 22 10:44:13 CET 2017

Thanks Ryan. I've determined the issue - a rather embarrassing one, 
actually, where the C array wasn't of the right length - I'm not quite 
sure why it didn't show up earlier. Anyway, patches have been committed 
to release and devel.



On 22/03/17 01:14, Ryan Thompson wrote:
> Hi Aaron,
> I'm making a ChIP-Seq analyisis pipeline using csaw, and I'm running
> into an inconsistent error/segfault. I've reduced it to a test case
> which you can find
> here: https://www.dropbox.com/sh/2a2vpb5ek4413fx/AAAXwCaTzsAmfyPefwAbFg8Na?dl=0
> The test case consists of my R workspace saved with save.image right
> before the code that causes the segfault along with a script that loads
> the workspace and then runs the offending code. The code consists of
> running combineOverlaps on each of a list of topTags tables. Seemingly
> at random, some but not all of the calls to combineOverlaps will fail
> and error, and occasionally R will segfault. Since the bug is random,
> I've also included a transcript of me running the script until it
> crashes, as well as a text file with the traceback in it.
> Can you help me debug the issue here?
> Thanks,
> -Ryan

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