Rscript Nextflow Error: unable to load shared object

Question

[Eliveri]

I have a nextflow DSL2 workflow which uses an Rscript in one of the processes and is run on a HPC cluster. I am getting the following error

Command error: processing file: myscript.Rmd Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/workflow_directory/work/conda/R_kn-fda2ff5d1d3670774376f8135a2c1a6e/lib/R/library/stringi/libs/stringi.so': libicui18n.so.58: cannot open shared object file: No such file or directory Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load Execution halted

The path to the .Rmd file is defined as a param in the config file.

Process like this:

  rscript = file(params.rscript)
  ...
   process run_report {
    ...
    input:
    ...
    path(rscript)
    output:
    ...
    script:
    """
   Rscript -e 'rmarkdown::render("myscript.Rmd")'
    """
}

Env file

name: R_kn
channels: 
  - defaults
  - conda-forge
dependencies: 
  - r-base=4.2.2
  - r-rmarkdown

[Marcel Ribeiro-Dantas]

According to a quick search I did, this is related (and a known issue) to the R package installed through conda-forge. Not really a Nextflow issue.

[Eliveri]

Thank you for the tip. I will look into it.