As long as paired is set to TRUE, it doesn't matter if the variance is equal or not. You'll get the same answer. That is because: Question 3 options: R doesn't know how to do paired t-tests A paired t-test sums everything down to one value (difference) so there's only one variance to look at, not two The tests actually are not the same, but they are so close that it's only their p-values that show they are different The tests actually are not the same, but they are so close that it's only their t-statistic that show they are different