Readline does wait for the user's input. But the problem is that, in your case, when you run all of your code at once, R will treat 'n2<-readline(prompt="Enter skip 2: " )' as the user's input (it indeed is) to the first readline. This is the root of the problem.
So basically you have two choices to deal with your problem, the first is to find some specific package in R that halts R execution process when prompting; the second one is to stick to the R base, but only use readline in the ending block of your file. In your case, you can use a little trick like this:
{
n1<-readline(prompt="Enter skip 1: " )
n2<-readline(prompt="Enter skip 2: " )
n1<-as.integer(n1)
n2<-as.integer(n2)
}
The rationale behind this trick is this: when R read the thing between { and }, it will treat all of the things in between as a whole command, this is the ending block of the code, so it behaves like what you want. R will not feed part of this command to another part of the command, thus prevents the problem you met.
You can develop similar tricks yourself, like putting the readline in a function:
foo <- function(){
n1<-readline(prompt="Enter skip 1: " )
n2<-readline(prompt="Enter skip 2: " )
n1<-as.integer(n1)
n2<-as.integer(n2)
c(n1, n2)
}
foo()
In this case, the whole foo function will act as the ending block of your code, and all things work as you want. Hope this helps.