You may try these gsub functions.
> gsub("[^\\d-]", "", x, perl=T)
[1] "123-456-789"
> gsub(".*\\(|\\)", "", x)
[1] "123-456-789"
> gsub("[^0-9-]", "", x)
[1] "123-456-789"
Few more...
> gsub("[0-9-](*SKIP)(*F)|.", "", x, perl=T)
[1] "123-456-789"
> gsub("(?:(?![0-9-]).)*", "", x, perl=T)
[1] "123-456-789"
