I've got the same error with your code when run in macOS or Windows 10.
You have cleanly formatted code in your post which helps, but a reprex actually runs the code so we can see the errors you are seeing. Here is your code in the form of a reprex.
V3<-c(1,2,3,4,5,6,7,NA,19,NA,98,NA,NA)
V4<-c("A",NA,"B",NA,"C",NA,"D",NA,"E","F","G",NA)
E<- complete.cases(V3,V4)
#> Error in complete.cases(V3, V4): not all arguments have the same length
E
#> Error in eval(expr, envir, enclos): object 'E' not found
V3[E]
#> Error in eval(expr, envir, enclos): object 'E' not found
V4[E]
#> Error in eval(expr, envir, enclos): object 'E' not found
Created on 2018-02-23 by the reprex package (v0.2.0).