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akundaje / phantompeakqualtools

Automatically exported from code.google.com/p/phantompeakqualtools
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Error : Protection stack overflow #2

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Dear all,

When runnning the script either on BAM or tagAlign files, I keep getting the 
same "protection stack overflow" error message (below).

As my background is biology and definitely not computer science, I'm not sure 
about what this means neither how I should deal with it.

Best regards from Montpellier, France.
Mathieu

[1] TRUE
Loading required package: caTools
Loading required package: bitops
Reading ChIP tagAlign/BAM file 
alignments/bowtie/align-Pm_20120529V/ChIP-K27ac_Pm_20120529V_m1.bam 
[bam_header_read] EOF marker is absent. The input is probably truncated.
opened /tmp/RtmpWmHbFe/ChIP-K27ac_Pm_20120529V_m1.tagAlign1e204556d5be
done. read 13778889 fragments
Error: protect(): protection stack overflow
Execution halted

Original issue reported on code.google.com by mathieu....@gmail.com on 16 Nov 2012 at 4:41

GoogleCodeExporter commented 9 years ago 
For R newbies like me, I solved my previous issue running the script with 
increased allocated protection stack memory :

Rscript --max-ppsize=500000 run_spp.R [options]

Original comment by mathieu....@gmail.com on 19 Nov 2012 at 12:31