[lstmemery]

I had a similar problem in a prediction pipeline a few years back. If I remember correctly, someone updated a R package to the next minor version. The package was to read an obscure file format. The fix installed a new C++ library. That C++ library somehow interacted with a second R package (using a specialized type of linear model) when compiled at source and all the results coming out of our package were subtly wrong but only with large files.

It turns out the way the second R package would determine the required precision of floats in sparse arrays was based on the compiled linear algebra libraries available. It took a week for us to debug and ultimately it was easier for us to just rewrite the whole thing in Python.

Renv has made things easier but I don't think packrat/renv allows you to lock C/C++ libraries as well as R ones.