[Bioc-devel] Duplicated method names in purrr and GenomicRanges

[O'CALLAGHAN Alan]

Hi,

Two options.

First option: import either purrr::reduce or GenomicRanges::reduce, and
call the other with [pkg]::reduce.

Second option: remove the import for both of these. Use purrr::reduce
and GenomicRanges::reduce to call both functions.

I think the second option leads to clearer code and would be my definite
preference.


On 12/09/2019 10:07, bioinf using posteo.de wrote:
> Dear all,
>
> I am developing a Bioconductor package and have a problem with two
> methods which have the same name. I am using the reduce() function
> from the R packages GenomicRanges and purrr. All methods from other
> packages are imported with @importFrom in all of my functions.
>
>
> During devtools::document() I get the following Warning:
>
> ...
>
> replacing previous import ‘GenomicRanges::reduce’ by ‘purrr::reduce’
> when loading ‘testPackage’
>
> ...
>
>
> Here are my NAMESPACE entries:
>
> # Generated by roxygen2: do not edit by hand
>
> export(mergeDataFrameList)
> export(reduceDummy)
> importFrom(GenomicRanges,GRanges)
> importFrom(GenomicRanges,reduce)
> importFrom(IRanges,IRanges)
> importFrom(dplyr,"%>%")
> importFrom(dplyr,left_join)
> importFrom(dplyr,mutate)
> importFrom(dplyr,pull)
> importFrom(magrittr,"%<>%")
> importFrom(purrr,reduce)
> importFrom(tibble,tibble)
>
>
> I am not using both reduce functions in the same function. To use the
> GenomicRanges reduce function, I have to call this function like this:
> GenomicRanges::reduce().
>
> I understand the warning and why I have to call the reduce function
> like this. Is there a solution for this problem? Compiling a R package
> with warnings and calling functions like this is not the best way I
> guess.
>
> I am using R version 3.6.1 (2019-07-05)
>
> Thanks for help!
>
> Best,
>
> Tobias
>
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