how to solve libgmp.so.10 error inside a biocontainer

how to solve libgmp.so.10 error inside a biocontainer

[Júlia Mir]

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Hi all,

I created a mulled biocontainer with pandoc and several R libraries, as it 
is a requirement for my R script. But when I try to use it, I get the 
following error:
/usr/local/bin/pandoc: error while loading shared libraries: libgmp.so.10: 
cannot open shared object file: No such file or directory 
204 
<https://github.com/nf-core/crisprseq/actions/runs/3900874470/jobs/6662044571#step:4:205> 
Error in system(paste(shQuote(pandoc_path), "--version"), intern = TRUE) : 
205 
<https://github.com/nf-core/crisprseq/actions/runs/3900874470/jobs/6662044571#step:4:206> 
error in running command 
206 
<https://github.com/nf-core/crisprseq/actions/runs/3900874470/jobs/6662044571#step:4:207> 
Calls: <Anonymous> ... get_pandoc_version -> with_pandoc_safe_environment 
-> force -> system 
207 
<https://github.com/nf-core/crisprseq/actions/runs/3900874470/jobs/6662044571#step:4:208> 
Execution halted

For example, when entering the docker container, I run:
docker run -it 
quay.io/biocontainers/mulled-v2-39480160ac5fd8ae2aaba8eb25795cb6f304e1ca:5e51897b0f9cc614dfec8ac1df8b960aeb75dfcd-0 
bash
/usr/local/bin/pandoc
and the output is:
/usr/local/bin/pandoc: error while loading shared libraries: libgmp.so.10: 
cannot open shared object file: No such file or directory

I have looked from some solutions, but all of them require installing 
different pandoc builds (
https://github.com/jgm/pandoc/issues/2774#issuecomment-196380657) or 
building the binary (
https://github.com/r-hub/rhub-linux-builders/issues/10#issuecomment-255916700), 
which, as far as I know, is not possible as I need it inside the mulled 
container which is created automatically.

I would appreciate if you can help me solve this problem. 

Thanks!
Júlia

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