Hi Sam, On 4/11/19 10:47, Samuela Pollack wrote: > 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?
Before their deprecation these methods should normally already be documented somewhere. In particular there should already be aliases and \usage entries somewhere for them. For example if foo() is the generic, the alias for the foo,SomeClass method is: \alias{foo,SomeClass-method} and the \usage entry for this method looks like this: \S4method{foo}{SomeClass}(x, ...) When deprecating this method, the \alias and \usage entry should be moved to the MyPkg-deprecated man page. Note that the "Function Deprecation Guidelines" only suggests to list the deprecated methods (and their replacements) in the \details section, but it's fine to also list them in a \usage section. > > (ii) Deprecating a S4 class. Should this look just like a function in > ThePkg-deprecated? Same as for a method except that, strictly speaking, there is no notion of \usage entry for an S4 class, only for its constructor function (if there is one). So the aliases for the class and its constructor, and the \usage entry for the constructor, should be moved to the MyPkg-deprecated man page. > > > (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. These are methods e.g. the [,SomeClass, [[,SomeClass, and [<-,SomeClass methods. The procedure to deprecate them is the same as for deprecating methods in general. So them as (i). Hope this helps, H. > > thanks, > > - Sam > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=c7mY7SviNf8WObwMM13uYGQuvB87RX3qS6eV5nIZsYg&s=QzjewaW8MNTVLiVirE1ytWId_dqFeUjSfYL5i6US2zM&e= > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel