To follow-up on what @manics said, see here and my next reply below in that discussion for an idea of why adding runtime.txt hijacks the R installation to make it incompatible with what is in your environment.yml. The first example I gave you didn’t refer to the import caveats discussed here about not mixing the approaches. There specifically addresses install.R; however, I think runtime.txt triggers that same process and so it is also incompatible, I believe.
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