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It works if you provide a factor type value on RHS of :=, this can be done with as.factor(NA) or even as.integer(NA) (because factor is of integer type):
DT[y=="", y:= as.factor(NA)]
But I agree to make sense to catch that automatically.
When trying to assign NA to a specfic items in a factor, an error is thrown, which does not happen in base DF.
R 3.3.0 DT 1.96
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