I'm trying to check if to DataFrame objects are identical.

My case in point:

    > d1 
DataFrame with 3 rows and 4 columns
                Name       BigWigPlus       BigWigMinus totalTags
         <character>      <character>       <character> <numeric> C547        C547 mm9.C547.plus.bw mm9.C547.minus.bw  12436172 C548        C548 mm9.C548.plus.bw mm9.C548.minus.bw  12277807 C549        C549 mm9.C549.plus.bw mm9.C549.minus.bw  14477276
    > d2 
DataFrame with 3 rows and 4 columns
                Name       BigWigPlus       BigWigMinus totalTags
         <character>      <character>       <character> <numeric> C547        C547 mm9.C547.plus.bw mm9.C547.minus.bw  12436172 C548        C548 mm9.C548.plus.bw mm9.C548.minus.bw  12277807 C549        C549 mm9.C549.plus.bw mm9.C549.minus.bw  14477276

These two look identical but:

> identical(d1, d2)
[1] FALSE

Coercing to a data.frame, they are identical:

> identical(as.data.frame(d1), as.data.frame(d2))
[1] TRUE

All individual columns are also identical:

> identical(d1$Name, d2$Name)
[1] TRUE
> identical(d1$BigWigPlus, d2$BigWigPlus)
[1] TRUE
> identical(d1$BigWigMinus, d2$BigWigMinus)
[1] TRUE
> identical(d1$totalTags, d2$totalTags)
[1] TRUE

The DataFrames haven't got anything store in the metadata slot.

What could explain this behaviour? What's the preferred way to compare DataFrame objects in this fashion?