[Bioc-devel] deprecation guidelines

Samuela Pollack @po||@ck @end|ng |rom j|mmy@h@rv@rd@edu
Thu Apr 11 19:47:08 CEST 2019

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 

(ii) Deprecating a S4 class. Should this look just like a function in 

(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.


- Sam

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