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") call. This is with netDx v1.3.1 which is in Bioc-devel release. Thanks,Shraddha -- 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 /tmp/RtmpbD9vyG/HWTSC5751L/ASD/part3/GM_results/CV_2.query [Thread 1] Processing /tmp/RtmpbD9vyG/HWTSC5751L/ASD/part3/GM_results/CV_3.query... finished computation - writing results [Thread 1] Finished /tmp/RtmpbD9vyG/HWTSC5751L/ASD/part3/GM_results/CV_3.query Performed 3 predictions in 2.90s --- finished re-building 'Predict_CaseControl_from_CNV.Rmd' --- re-building 'ThreeWayClassifier.Rmd' using knitr *** buffer overflow detected ***: terminated [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel