data.table objects assigned with := from within function not printed

As David Arenburg mentions in a comment, the answer can be found here. There was a bug fixed in the version 1.9.6 but the fix introduced this downside.

One should call DT[] at the end of the function to prevent this behaviour.

myfunction <- function(dt) {
    dt[, z := y - x][]
}
myfunction(mydt)  # prints immediately
#    x y z
# 1: 1 5 4
# 2: 2 6 4
# 3: 3 7 4 

This is described in data.table FAQ 2.23:

Why do I have to type DT sometimes twice after using := to print the result to console?

This is an unfortunate downside to get #869 to work. If a := is used inside a function with no DT[] before the end of the function, then the next time DT is typed at the prompt, nothing will be printed. A repeated DT will print. To avoid this: include a DT[] after the last := in your function. If that is not possible (e.g., it's not a function you can change) then print(DT) and DT[] at the prompt are guaranteed to print. As before, adding an extra [] on the end of := query is a recommended idiom to update and then print; e.g.> DT[,foo:=3L][].