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

[Hervé Pagès]

On 10/31/23 07:22, Wolfgang Huber wrote:

> 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 Hervé to add ‘results' to BiocGenerics and everyone who exports such a function converts it to a method for that generic.

My pleasure, and that's the cleanest solution. But it will only help if 
the package that defines the "other" results() function is a 
Bioconductor package and not a CRAN package. Has this package been 
identified?

A 4th option is to make sure that the other package gets loaded _before_ 
SNPhood e.g. by putting an explicit library(<the other package>) before 
library(SNPhood) in your vignette, even though that's kind of hacky.

Best,

H.

>
> Thank you and kind regards
> Wolfgang
>
> --
> Wolfgang Huber
> EMBL
> https://www.huber.embl.de/
>
>
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>
>> 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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-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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