From the documentation of install.packages()
destdir
directory where downloaded packages are stored. If it is NULL (the default) a subdirectory downloaded_packages of the session temporary directory will be used (and the files will be deleted at the end of the session).
It says the files will be deleted at the end of the R session, but you can specify the folder using that parameter if you want.
This shouldn't be something to worry about, if you had so little space in your disk for this to be a problem you wouldn't be able to make any practical use of R either.