Thanks for explaining the context. It helps to understand what Bioconductor developers expect.
> On 05/12/2017 07:11 AM, Martin Morgan wrote: > > On 05/12/2017 02:05 AM, Garth Ilsley wrote: > >> Hello, > >> > >> I am thinking of creating package for Bioconductor, and I am > >> wondering about the use of R6 classes (from the R6 package). I do > >> indeed intend to use existing Bioconductor classes such as > >> SummarizedExperiment and interact and make use of other Bioconductor > >> packages, such as scater and DESeq2. This appears to be in accordance > >> with the guidelines > >> (https://www.bioconductor.org/developers/package-guidelines/#classes) > >> , but does the use of R6 classes disqualify the package from being in > >> Bioconductor? Do I need to write my classes as S4 in order to qualify? > >> > > > > I think there's little value in exposing R6 classes to Bioconductor > > users, introducing yet another syntax and semantics, and would > > strongly discourage their use outside the package name space. > > > > Inside the package name space the maintainer has more liberty to adopt > > programming practices that are geared toward correct and efficient > > implementations; if R6 fills this role (I'm not an expert, but I don't > > think R6 enforces strong type checking and is not particularly > > efficient) then it would be appropriate to use them. > > Maybe one additional point is that perhaps 'write my classes' implies that > you'll be creating new classes; it might often be better to re-use existing > classes, or worst-case write simple extensions (e.g., an additional slot to > SummarizedExperiment) to existing classes. In this way you re-use existing > robust software and don't further overwhelm the cognitive burden placed on > the user struggling to navigate yet more functionality. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
