Error : Protection stack overflow

[GoogleCodeExporter]

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]

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

[varunorama]

Hello,

I have been running into the same problem as above, and have tried the potential solution presented above. I have also tried adding

options("experssion" = 500000)

as mentioned here: kundajelab/phantompeakqualtools#3

These solutions did not work as expected and I still run into the error:
Error: protect(): protection stack overflow
Execution halted

Any ideas on why this error is persisting? For full disclosure, the genome that I am working with has a LARGE number of scaffolds and is not a chromosome assembly.

Thank you!

[jammywwh]

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

It Works! Thx. Love you.