[Bioc-devel] providerVersion error with BSgenome genomes

[Diego Diez]

Finally, I found this which might be a suitable option:

metadata(BSgenome.Dmelanogaster.UCSC.dm3)$genome
>"dm3"

But happy to hear about alternatives.

Best,
Diego

On Sat, Jul 18, 2020 at 12:56 AM Diego Diez <diego10ruiz using gmail.com> wrote:
>
> 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