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

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 at 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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