What output do you get from
.libPaths()
I get
[1] "/home/fjcc/R/x86_64-pc-linux-gnu-library/3.5" "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library" "/usr/lib/R/library"
I have seen the library paths get corrupted and then packages could not be found or installed.