Depending on what you're doing in the loop, the fact that the %in% operator returns a vector might be an issue; consider a simple example:
c1 <- c("one","two","three","more","more")
c2 <- c("seven","five","three")
if(c1%in%c2) {
print("hello")
}
then the following warning is issued:
Warning message:
In if (c1 %in% c2) { :
the condition has length > 1 and only the first element will be used
if something in your if statement is dependent on a specific number of elements, and they don't match, then it is possible to obtain the error you see