[Bioc-devel] providerVersion error with BSgenome genomes

[Diego Diez]

I found that the providerVersion method has been deprecated (see
commit log below). Is there an official way to obtain that information
now? I could do unique(genome(dm3)) but not sure if this is the best
approach.

Diego

commit f99ceb5d17ca6dcf886600bf1fbf5d7c398de75c
Author: Hervé Pagès <hpages using fredhutch.org>
Date:   Fri Jun 26 18:49:17 2020 -0700

    A couple of changes to GenomeDescription objects

    - The GenomeDescription() constructor looses its 'provider_version'
      argument.
    - The providerVersion() accessor is now deprecated.

On Sat, Jul 18, 2020 at 12:46 AM Diego Diez <diego10ruiz using gmail.com> wrote:
>
> To add more information, this is what I get for
> showMethods("providerVersion") using Bioc 3.11:
>
> >showMethods("providerVersion")
> Function: providerVersion (package GenomeInfoDb)
> x="BSgenome"
>     (inherited from: x="GenomeDescription")
> x="GenomeDescription"
> x="GFFFile"
> x="SNPlocs"
> x="XtraSNPlocs"
>
> But with Bioc devel I get:
>
> showMethods("providerVersion")
> Function: providerVersion (package GenomeInfoDb)
> x="GenomeDescription"
> x="GFFFile"
> x="SNPlocs"
> x="XtraSNPlocs"
>
> So it seems providerVersion has lost the BSgenome method. Is this an
> intentional change or something that needs to be fixed?
>
> Thank you.
> Diego
>
> On Thu, Jul 16, 2020 at 2:38 PM Diego Diez <diego10ruiz using gmail.com> wrote:
> >
> > Dear all,
> >
> > I am finding an error when running the following code:
> >
> > > library(BSgenome.Dmelanogaster.UCSC.dm3)
> > Loading required package: BSgenome
> > Loading required package: GenomeInfoDb
> > Loading required package: GenomicRanges
> > Loading required package: rtracklayer
> >
> > > dm3 <- BSgenome.Dmelanogaster.UCSC.dm3
> > > providerVersion(dm3)
> > Error in (function (classes, fdef, mtable)  :
> >   unable to find an inherited method for function ‘providerVersion’
> > for signature ‘"BSgenome"’
> >
> > > BiocManager::version()
> > [1] ‘3.12’
> >
> >
> > I am expecting to get "dm3" with this genome. What would be the proper
> > way to do this?
> >
> > Thank you.
> >
> > Best,
> >
> > Diego