Thanks @MSullivan!
Based on the .libPaths() output, it looks like the instructions should still generally work. I think what might be wrong is your file doesn’t seem to end with a newline. I’m not sure how much that matters to R, but just in case, run the following:
echo ".libPaths(.libPaths()[2])" > ~/.Rprofile
That should dump exactly one line (with a newline character) overwriting whatever’s in .Rprofile at the moment.
Let me know if that helps, otherwise, if you could post the result of running --verbose on the dada2 denoise command that is currently failing, that would be great!