[Bioc-devel] Whether to copy unexported BSgenome function into multicrispr

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Wed Aug 28 18:32:48 CEST 2019

Hi Aditya,

I've added the 'load.only' argument to getBSgenome(). This is in 
BSgenome 1.53.2. See 

This change will propagate to BioC devel in the next couple of days.


On 8/28/19 02:18, Bhagwat, Aditya wrote:
> Dear BioC developers,
> BSgenome::getBSgenome('mm10') returns BSgenome.Mmusculus.UCSC.mm10::Mmusculus.
> But that function also attaches BiocGenerics, S4Vectors, IRanges and Biostrings, which is unfortunate from a keep-the-namespace-clean perspective.
> I could instead use the clean alternative
> bsname <- BSgenome:::.getInstalledPkgnameFromProviderVersion('mm10')
> utils::getFromNamespace(bsname, bsname)
> But that, off course, (BioC)Check does not like, since using unexported functions doesn't fit into the R software development paradigm.
> So then instead I could copy paste the latter function into my multicrispr <https://urldefense.proofpoint.com/v2/url?u=https-3A__loosolab.pages.gwdg.de_software_multicrispr_index.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=NLEmi2kgNId0qr_WzhgCW7yISIMUIwqxFyIuhaG6Zos&s=nKk9IYRWMx9XmPMxAhoUnFqSmPsHtZsmKqmdzNu9aBs&e= > package (which is being readied for BioC) and add its author, Herve Pages, as a co-author of my package (after, off course, informing him). Is this the way such things are normally dealt with? Or how would you guys deal with a situation like this?
> A function-level question regarding this topic was posted earlier on BioC support<https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_123709_-23123711&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=NLEmi2kgNId0qr_WzhgCW7yISIMUIwqxFyIuhaG6Zos&s=BaqrQswG_I6dbFqDIT5n_rkPCDEOg7OYRs5SD7DMU_o&e= >. The current question is more of a package development question, though, and I thought it would be nice to get feedback from more experienced BioC developers :-)
> Thank you for your feedback!
> Aditya
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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