Dear Bioconductor,
We are deprecating part of a package. I am following the guidelines in
the "Function Deprecation Guidelines" page at bioconductor.org and I
have a few questions:
(i) Deprecating a S4 method which has the same name in another S4 class.
We have two DelayedArray backends. Functions like dim and dimnames are
deprecated in one but not in the other. Should those functions be listed
in the ThePkg-deprecated document? With the name of the backend that's
being deprecated? With a note about the backend that is *not* being
deprecated?
(ii) Deprecating a S4 class. Should this look just like a function in
ThePkg-deprecated?
(iii) subscript, double-subscript, assign-to-property (property<-)
operators. Should they be included in ThePkg-deprecated.Rd? In favor:
they are being deprecated for the class they pertain to. Against: we
certainly aren't deprecating the subscript operator in general.
thanks,
- Sam
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