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vjcitn / ontoProc

https://vjcitn.github.io/ontoProc
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Indirect Dependency on owlready2 Causing R CMD Check Failures #17

Open AlmogAngel opened 5 days ago

AlmogAngel commented 5 days ago

Hello, I am developing a package that depends on ontoProc, and I’m encountering an issue during R CMD check due to the indirect dependency on the Python package owlready2:

Error in py_module_import(module, convert = convert) : 
  ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Using virtual environment 'r-owlready2' ...
+ /home/pkgbuild/.virtualenvs/r-owlready2/bin/python -m pip install --upgrade --no-user owlready2
Requirement already satisfied: owlready2 in /home/pkgbuild/.virtualenvs/r-owlready2/lib/python3.12/site-packages (0.46)
Warning messages:
1: In check_forbidden_install("Python packages") :
  cannot install Python packages during R CMD check
2: In check_forbidden_install("Python packages") :
  cannot install Python packages during R CMD check

Since both ontoProc and my package are Bioconductor packages, I would appreciate any guidance on how to handle this dependency properly within the Bioconductor ecosystem to avoid check failures.

Thank you for your help!

vjcitn commented 5 days ago

would you please tell me the URL of repo of your package in development? i would like to understand what features of ontoProc you are using

AlmogAngel commented 5 days ago

would you please tell me the URL of repo of your package in development? i would like to understand what features of ontoProc you are using

I am using ontoProc within this funciton: https://github.com/AlmogAngel/xCell2/blob/master/R/xCell2GetLineage.R