I recently updated R from 3.6.1 to 4.0.2. Along with that, I updated to the latest version of rtools (rtools40). I also followed instructions to add rtools40 to the PATH here.
However, after restarting R, Sys.which("make") gives "C:\\Rtools\\bin\\make.exe", an older version of Rtools. But C:/Rtools/bin is not in my PATH.
Without deleting the old rtools, how can I tell R to use rtools40?
Edit: It turns out that the old Rtools was on the system PATH (but not on the user PATH). Removing the old Rtools/ from system PATH fixed the issue.
Posting my comment as an answer, so that others may more easily find the solution:
When updating from Rtools to Rtools40, make sure that the old Rtools is removed from the system and user PATH. In order to check which version you have in your path, you can use Sys.which("make") like you suggested in your question.
It is also possible to check by running Sys.getenv("PATH").