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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=NLEmi2kgNId0qr_WzhgCW7yISIMUIwqxFyIuhaG6Zos&s=lhIl9G558NPHogQPe0cIqqd7f8TlIwfaALsP03D2dis&e= > -- 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: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel