In order to remove the warning message, you can do the following to import both packages,
@rawNamespace import(GenomicRanges, except=�reduce�) @importFrom purrr reduce Then the NAMESPACE of direct "reduce" call will be reserved only to the package of "purrr". Which means that when you do "reduce()", this function refers to the "purrr", When you use the reduce function from GenomicRanges, you have to use "GenomicRanges::reduce". ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Michael Lawrence via Bioc-devel <bioc-devel@r-project.org> Sent: Thursday, September 12, 2019 7:05 AM To: O'CALLAGHAN Alan <A.B.O'callag...@sms.ed.ac.uk> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] Duplicated method names in purrr and GenomicRanges Third option: use Reduce() from base instead of purr::reduce(). On Thu, Sep 12, 2019 at 2:54 AM O'CALLAGHAN Alan <A.B.O'callag...@sms.ed.ac.uk> wrote: > > 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, bio...@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 > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > The University of Edinburgh is a charitable body, registered in Scotland, > with registration number SC005336. > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Michael Lawrence Scientist, Bioinformatics and Computational Biology Genentech, A Member of the Roche Group Office +1 (650) 225-7760 micha...@gene.com Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]]
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