Turns out when I installed RTools I left out the R 2.15.x+ toolchain option in the installation, which lead to the gcc never being installed. Hopefully, this post will serve as a diagnostic guide if RStudio fails to register RTools.

Thank you everyone for your help.

There are many questions and answers about Rtools not being installed and/or not being recognized by R. Most of these answers talk about some of the portions:

• Rtools not being detected by R
• Rtools not found by R when installing packages from CRAN
• How do I get Rtools 3.0 working for R 3.0? R can't find the installation
• Installing ggplot2 after installing rtools
• Rtools not found by R when installing packages from CRAN

But generally no answer contains this: Restart R. Some say to restart RStudio, which for most users is good enough, but not everybody runs RStudio (gasp!), and even so the need to restart it is not stated loudly enough.

So here are some steps for dealing with Rtools not being found on Windows.

1. Go to https://cran.r-project.org/bin/windows/Rtools/ and go to the correct version of Rtools (based on your version of R), and follow its links for downloading it and installing it. This is a windows installation, not an R package, so install it like you would another app in windows: double click the downloaded file.

2. If you installed to a default location, then it should take care of updating the Windows PATH variable for you. If you installed to a non-standard location, then you may need to change the apparent PATH (at least for your R processes). These answers talk about various ways to work through this, though some might be outdated or not applicable to your specific problem. There are countless other StackExchange questions about updating the system PATH, don't take this as an exhaustive or even canonical approach.

   • https://stackoverflow.com/a/62469982/3358272
   • https://stackoverflow.com/a/64170944/3358272
   • https://stackoverflow.com/a/69843978/3358272

3. Restart R. If you're running in RStudio, restart RStudio as well. In fact, whatever IDE you're using may need to be restarted completely. It might even be necessary (if using a corporate computer with stricter group policies) to log out and log back in. Frankly. that last one should not be necessary in modern times, but I say it so that if restarting R and RStudio (or VScode) do not do it for you, please try logging out and back in. It doesn't sound like it should work, sometimes it does. (Just like when calling Tech Support on something, they often say "reboot" hoping to get lucky, because sometimes that fixes things.)

4. Check Sys.which("make") to see that is should no longer be empty. From here, package installation for packages needing compiling should just work.

The most common mistakes I've seen:

• thinking Rtools is an R package, it is not, install.packages("Rtools42.exe") will never work
• skipping step 3

(Community: if I'm skipping steps, feel free to suggest edits to this to fill it out. If I missed a clearly-superior answer, please either add it to this answer or let me know and we can find better ways to redirect.)

I have sorted the problem in this way, partly guided by the comments on the question at:

Rtools not being detected by R

Given that devtools::find_rtools() returns TRUE and the check at the end of this webpage using Rcpp (https://thecoatlessprofessor.com/programming/installing-rtools-for-compiled-code-via-rcpp/) works:

Try Sys.which("ls.exe") and Sys.which("gcc.exe"). The former should return a path, but the latter may be empty, which is the problem.

I then found another copy of gcc.exe (in my case it there was one at C:\Rtools\mingw_64\bin, which is a bit maddening) and copied it into C:\Rtools\bin, which is where RStudio seems to want it. That is where ls.exe was found using the Sys.which. That solved the problem for me.