[Bioc-devel] Package problems due to results() function from other package?

[Julien Wollbrett]

Hi,

Sorry... it looks like I replied to the wrong email....
________________________________
De : Bioc-devel <bioc-devel-bounces using r-project.org> de la part de Julien Wollbrett <julien.wollbrett using unil.ch>
Envoyé : mardi 31 octobre 2023 16:04
À : Wolfgang Huber <wolfgang.huber using embl.org>; Christian Arnold <chrarnold using web.de>
Cc : bioc-devel using r-project.org <bioc-devel using r-project.org>
Objet : Re: [Bioc-devel] Package problems due to results() function from other package?

Bonjour,


Quelle magnifique nouvelle.


Nous ne serons malheureusement pas disponible avant le 30 novembre car nous partons ce vendredi pour un mois de vacances dans nos familles respectives.Nous serions potentiellement disponibles demain ou jeudi mais j'imagine que cela n'est pas du tout compatible avec votre planning.

Est ce qu'il serait possible de vous rencontrer en d�cemb ou est ce que notre absence risque de nous causer pr�judice pour la place en

________________________________
De : Bioc-devel <bioc-devel-bounces using r-project.org> de la part de Wolfgang Huber <wolfgang.huber using embl.org>
Envoy� : mardi 31 octobre 2023 15:22
� : Christian Arnold <chrarnold using web.de>
Cc : bioc-devel using r-project.org <bioc-devel using r-project.org>
Objet : Re: [Bioc-devel] Package problems due to results() function from other package?

Dear Christian

If your vignette attaches another package that exports a �results� function, after it attached SNPhood which defines its own results function, then the R interpreter has no other choice than doing what it does.

Other people adding additional functionality to their packages is probably not something one can really complain about, so I see three options
- you use SNPhood::results in your vignette
- you don�t attach the other package, and rather just use what you need from it using �::�
- you convince Herv� to add �results' to BiocGenerics and everyone who exports such a function converts it to a method for that generic.

Thank you and kind regards
Wolfgang

--
Wolfgang Huber
EMBL
https://www.huber.embl.de/









> Il giorno 2023-10-28, alle ore 16:15, Christian Arnold <chrarnold using web.de> ha scritto:
>
> For my package SNPhood that did not receive any code changes or updates
> in quite a while, I suddenly see errors with Bioc 3.18:
> https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/SNPhood/nebbiolo2-buildsrc.html
>
> Error: processing vignette 'workflow.Rmd' failed with diagnostics:
> unused argument (type = "allelicBias")
>
> This comes from this line I think:
>
> names(results(SNPhood.o, type = "allelicBias"))
>
> For literally years, this didnt cause any problems, and the results
> function is actually (re)defined in the SNPhood package:
>
> results <- function(SNPhood.o, type, elements = NULL)
>
> I am not sure now what causes this. Should I use the syntax
> SNPhood::results to make it clear, or I am wrongly assuming that the
> wrong result function is taken that causes the error?
>
> Any pointers?
>
>
> Best
>
> Christian
>
>
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>
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