[Bioc-devel] Deprecated a contained class

Hervé Pagès hp@ge@ @end|ng |rom |redhutch@org
Fri Jun 26 19:17:04 CEST 2020

Hi Martin,

Don't know how/where to implement a deprecation message that wouldn't be 
confusing for the end users.

FWIW if the replacement of class Original with class New is just a 
renaming (everything else remains the same), a situation I've dealt with 
a lot in the S4Vectors/IRanges/GenomicRanges infrastructure, I like to 
use the following pragmatic approach:

In package A:

   ## Replace Original with New in the Original class definition.
   setClass("New", ...)

   ## Define Original as an "alias" for New:
   setClass("Original", contains="New", representation("VIRTUAL"))

Then contact maintainers of packages that implement subclasses of 
Original that they should use New instead of Original. They can take 
their time because the cost of keeping the Original alias around is 
virtually zero.


On 6/26/20 08:10, Martin Morgan wrote:
> Pkg A provides a (virtual) class "Original".
> Pkg B creates a derived class setClass("Derived", contains = "Original")
> Pkg A would like to deprecate "Original" and replace with "New".
> Any ideas on how to implement a deprecation message so that the Pkg B maintainer knows that their use of class Original is deprecated, but users aren't bothered by more-or-less incomprehensible messages on use? I guess using .Deprecated() somehow associated with setClass(); implementing something in initialize,Original-method would be too irritating to the user.
> Thanks,
> Martin
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ZKKJsd3wTpxv3iRPiOQc8jk8ptFPwzh5TRNm8J6qDvA&s=TPnb__JeD-SoYXG79uR2hkfYDjmT6apkCdSfqyF1bKA&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: hpages using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

More information about the Bioc-devel mailing list