From: "Júlia Mir" <mirp.julia-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
To: pandoc-discuss <pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
Subject: how to solve libgmp.so.10 error inside a biocontainer
Date: Thu, 12 Jan 2023 02:12:03 -0800 (PST) [thread overview]
Message-ID: <b0081f7e-86d7-4025-ae65-561d6871265en@googlegroups.com> (raw)
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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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