[r] Use .Deprecated for used_shape in R

[johnkerl]

Follow-on from #2834 (comment) for issue #2407

Example interactive use:

> exp <- SOMAExperimentOpen('/var/p')

> exp$ms$get("RNA")$X$get("data")$used_shape()
$soma_dim_0
integer64
[1] 0    2637

$soma_dim_1
integer64
[1] 0    1837

Warning message:
used_shape will be removed in TileDB-SOMA 1.14

[mojaveazure]

Looks good to me! .Deprecated() works by throwing warnings that are classed as deprecatedWarning; given that testthat will throw warnings if it catches warnings where they aren't expected (expect_warning()), I've added suppressions of deprecations in the tests in c52bdbf

[johnkerl]

TIL, thanks @mojaveazure !