Error in dyn.load(file, DLLpath = DLLpath, ...) :

Question

[Hayler Edu]

Hello

I'm trying to do a AnalyzeCovariates but I have an error when I try to get the AnalyzeCovariates.pdf archive.

This is the error:

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/media/HDD1/Edu/miniconda3/envs/GATK4/lib/R/library/stringi/libs/stringi.so':
  libicui18n.so.64: cannot open shared object file: No such file or directory
Calls: source ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
In addition: Warning messages:
1: In eval(ei, envir) : NAs introduced by coercion
2: In eval(ei, envir) : NAs introduced by coercion
Execution halted

And this is my pipeline:

gatk AnalyzeCovariates -before SEC9.table -after SEC9_post_recal_data.table -plots AnalyzeCovariates.pdf

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.

Answer 1

[Ram]

Looking at your error message (and your post history), I'm making a few assumptions. Correct me if any of them is wrong:

1. You are using GATK installed through conda
2. You had a problem with Rscript previously so you have installed R through conda as well

If the above are true, the error message indicates that the R package stringi is missing in your conda env. From the terminal, install the r package stringi in your GATK env:

conda install -n GATK4 -c conda-forge r-stringi