Message-ID: <1e17b072-e6ae-5003-4584-41204ba0532b@fredhutch.org>
Date: 2019-08-28T16:32:48Z
From: Hervé Pagès
Subject: [Bioc-devel] Whether to copy unexported BSgenome function into multicrispr
In-Reply-To: <0BAB1337882A904E88F6957DE74DBC453C4B3881@KI-S0113.kerckhoff.mpg.de>
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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--
Herv? Pag?s
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 at fredhutch.org
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