[Bioc-devel] basilisk falling back to pip and breaking environment setup

[Rodrigo Arcoverde Cerveira]

Hi basilisk team,

First, thank you for your continued work on basilisk and for the fixes and improvements in recent versions. Also thanks to Vincent for the helpful replies to my previous questions.

I�ve recently run into an issue where basilisk seems to fall back to using pip (via reticulate:::pip_install(python, packages)) instead of setting up the environment with conda, even when all packages are available via conda. This is happening in packages like scifer, MOFA2, and pirat, which previously built fine. Now, builds fail with errors when trying to install packages that are supposed to install via conda but fall on pip.

The basilisk environment definitions still specify conda packages and channels (bioconda, conda-forge), and nothing has changed there. Has something changed in how basilisk sets up environments or handles fallbacks?

Would appreciate any guidance on how to make sure conda is used as expecte


Best,
Rodrigo

--
Rodrigo Arcoverde Cerveira
PhD student in Karolinska Institutet, Sweden
Karin Lor�s research group
CMM L8:00, Visionsgatan 18




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