This use derives from the radio alphabet used by the US Navy in WWII, in which the word Roger was the phonetic representation of the letter R, ('R' as in 'Received').
Nowadays, the accepted phonetic representation of R is Romeo, from the NATO radio alphabet, but once a radio operator gets used to 'rogering', it's a hard habit to break.
Rog"er (?), n. [From a proper name Roger.]
A black flag with white skull and crossbones, formerly used by pirates; -- called also Jolly Roger.
© Webster 1913
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