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build: check sub-environment r.yaml #117

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deliaBlue opened this issue Nov 4, 2023 · 1 comment
Open

build: check sub-environment r.yaml #117

deliaBlue opened this issue Nov 4, 2023 · 1 comment

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@deliaBlue
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When running the workflow via Conda, this message appears:

Environment for /home/XXXX/mirflowz/workflow/envs/python.yaml created (location: .snakemake/conda/acfa1a6f2c679a65546a19fba8898208_)
Creating conda environment /home/XXXX/mirflowz/workflow/envs/r.yaml...
Downloading and installing remote packages.
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working...  
To install TinyTeX with `tinytex::install_tinytex()` the system must have a functional Perl
installation with a `File::Find` module. Most end-user systems will already satisfy this
requirement; however, some minimal contexts (e.g., containers) may not. Perl is available
via Conda Forge as the package `perl`. See https://github.com/rstudio/tinytex/issues/419
 
done

TinyTex is -in principle- not used in the workflow therefore this warning is related to some dependencies within r.yaml that might - or might not - affect the end result and the workflow behavior.
Check the dependencies and requirements for the sub-environment r.yaml and its relation to the R scripts to fix this.

@uniqueg
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uniqueg commented Nov 8, 2023

Thanks. And yes, to fix it:

  • Either remove the TinyTex dependency, or whatever requires TinyTex, if it does not affect the workflow results
  • Or add perl to r.yaml as described

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