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

[Pages, Herve]

Hi Aditya,

I've added the 'load.only' argument to getBSgenome(). This is in 
BSgenome 1.53.2. See 
https://github.com/Bioconductor/BSgenome/commit/0eeddb5c0f57c69a0db31874b7b031ba06720bee

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

Cheers,
H.

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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> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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