Error: protect(): protection stack overflow

[Pooran-Dewari]

hello,

I am running nf core ChIPseq pipeline using nextflow and docker. I get the follwoing error after which the pipeline aborts.

Command error:
Loading required package: Rcpp
Error: protect(): protection stack overflow
Execution halted

command:

nextflow run nf-core/chipseq --input design_pe.csv --genome AtlanticSalmon \
-profile docker -c config_Ss --macs_gsize 2700000000 --narrow_peak True \
--clip_r1 20 --clip_r2 20 --three_prime_clip_r1 10 --three_prime_clip_r2 10 \
--max_cpus 16

It runs for some hours and then throws this error (attached error report)
pipeline_report.txt:

thanks for your help

ps: I suspect it has something to do with https://stackoverflow.com/questions/32826906/how-to-solve-protection-stack-overflow-issue-in-r-studio but I am not sure how to achieve this on R (not rstudio).

[JoseEspinosa]

After Slack discussion, @drpatelh created this branch that set the option --max-ppsize=500000 that allows increasing the size of the protect call stack and solves this issue. See here.

[JoseEspinosa]

Fixed in #269, now the module accepts arguments and thus the --max-ppsize=500000 can be passed using a config file as the one below:

process {
  withName: 'PHANTOMPEAKQUALTOOLS' {
    ext.args   = '--max-ppsize=500000'
  }
}