My question is asking regarding a specific observation that I would like to understand.

I just tried to install the package rJava in R and failed even though I prefaced the installation as suggested by the manual with:

sudo R CMD javareconf

Then I came across this comment:

Using sudo and running as root are not exactly the same thing. – Jon7

Desparate as I was I tried it:

sudo su
R CMD javareconf

And to my surprise I suddenly could install that package.

Sorry for the lenghty introduction but I wanted to give you a context to prevent answers like here. The question does not aim at specifically the described observation - rather at those "things" in general on Ubuntu.

My question is: How could this be possible? What is the difference between sudo X and runnding X as root?