I would like to use the following code to get exon annotation within my package

genes <-  AnnotationDbi::keys(Mus.musculus, "GENEID")
exon_data <- AnnotationDbi::select(
    Mus.musculus,
    keys = genes,
    keytype = "GENEID",
    columns = c(
        "GENEID",
        "TXID",
        "EXONCHROM",
        "EXONSTRAND",
        "EXONSTART",
        "EXONEND",
        "SYMBOL"
    )
)

However I want to do this without loading in the Mus.musculus package. Simply getting the Mus.musculus object from the package using getFromNamespace is not enough to make this work. I could library it inside the function and detach it before return, but this has the unwanted side-effect that users with Mus.musculus already loaded will find it detached after running my function.

This bug has been fixed in the 'devel' branch, version 1.31.1 (available in 48 hours), where Mus.musculus::Mus.musculus now works.

It is better to ask questions about package development on the bioc-devel mailing list.