where does the downloaded file gets stored in the R-Studio Server on Ubuntu EC2 Instance when using download.file()
It'll put it exactly where you asked for it:

 destfile = "Haberman.txt"


that is, a file called Haberman.txt in the current working directory at the time you ran download.file. You can get the current working directory with getwd() in R.

So for example if its something you can read with read.csv, you can do:

hdata = read.csv("Haberman.txt")


as long as you haven't changed the current working directory (like with setwd).