Hello ava, I am having a similar problem. I originally had R version 3.6 and recently upgraded to R version 4.0. I have been getting: Failed to install 'leidenbase' from Github: System command 'Rcmd.exe' failed, exit status:1, stout + stderr empty. Even my install.packages() fails for crayon and dplyr on R Studio. I've tried changing CRAN mirrors, security measure for downloading packages, and still nothing has worked. Hope we can solve this soon.
Update: In my case at least, I have narrowed down that any packages that need to build from a tar.gz (source) fail but not with a .zip (binary). It is able to download the tar.gz and save it to the temporary location, but it fails at the next step. Not sure, if you've found a solution, but I'll let you know if I do.
Update 2: I ended up doing a hard reset of my PC. It was a fairly new laptop, so everything was pretty much backed up. Windows 10 has an option to delete apps, files, and presets, and redownload windows from the cloud. For me, it took less than an hour to reset. I redownloaded R version 4.0.3, Rtools40 (following the adding it to your path with .Renviron), and then R studio 1.4.1103. I was able to upgrade to all new packages, and use devtools to install Monocle3 software without issue. It's definitely a drastic measure and I wouldn't want to do this again, so if you do figure out an alternative to your problem, I'd really love to know! Thank you!