[Bioc-devel] segfault in csaw native code

Ryan Thompson rct at thompsonclan.org
Wed Mar 22 02:14:29 CET 2017

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:

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?



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