[Bioc-devel] Switch to rJava - "buffer overflow detected" error

Shraddha Pai @hr@ddh@@p@| @end|ng |rom utoronto@c@
Fri Nov 20 14:34:16 CET 2020

Hello BioC community,
Our package netDx makes Java calls; to support Win machines and various
Java flavours I recently switched from system2() java calls to rJava.

Now my vignettes crash with a "buffer overflow detected" error, followed by
a core dump. Error below this email

I don't think it's a memory issue because in my zzz.R file I'm assigning
10Gb to Java heap space.

I would appreciate any insights to help debug the issue.All these vignettes
were working on OS X and Unix machines, with the previous system2("java")

This is with netDx v1.3.1 which is in Bioc-devel release.

Shraddha Pai, PhD
http://shraddhapai.com ; @spaiglass on Twitter
Post-doctoral Fellow, http://baderlab.org
The Donnelly Centre for Cellular and Biomolecular Research
University of Toronto
On bioc-devel Docker:

$ R CMD build netDx
[Thread 1] Finished
[Thread 1] Processing
finished computation - writing results
[Thread 1] Finished
Performed 3 predictions in 2.90s
--- finished re-building 'Predict_CaseControl_from_CNV.Rmd'

--- re-building 'ThreeWayClassifier.Rmd' using knitr
*** buffer overflow detected ***: terminated

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