[Bioc-devel] providerVersion error with BSgenome genomes

[Diego Diez]

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