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(Testing on an old version of data.table, but figured I'd file since I didn't see any issues filed on it and still see the same code up, missing calls to unique/funique.) EDIT: Just upgraded and am seeing the same behavior.
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@jangorecki just noticed you've self assigned this. I've just created a new branch with plans to add the all argument to fsetequals so that all = FALSE ignores duplicate rows. Do you want me to delete the branch and leave for you to resolve instead?
(I guess you know but...) setequal in base behaves that way not because it counts dupe rows, but because it regards columns as the elements of the set instead of rows. So setequal(transpose(df1), transpose(df2)) is true.
It also does other wonky/undesirable stuff when not working with vanilla vectors: