[Bioc-devel] [bug] goseq fails when dplyr has been loaded

[Keith Hughitt]

(patch with above change...)


On Sat, Jul 12, 2014 at 10:07 PM, Keith Hughitt <keith.hughitt at gmail.com>
wrote:

> To reproduce, load goseq followed by dplyr and call the "goseq" function.
>
> Example output:
>
> Error in UseMethod("select") :
>   no applicable method for 'select' applied to an object of class
> "c('GODb', 'AnnotationDb', 'envRefClass', '.environment', 'refClass',
> 'environment', 'refObject', 'AssayData')"
> Calls: render ... withCallingHandlers -> withVisible -> eval -> eval ->
> goseq -> select
>
>
> Unloading dplyr resolves the issue:
>
>     detach("package:dplyr", unload=TRUE)
>
> Tested in Bioconductor-devel (3.0) + goseq-svn (92448 2014/06/26).
>
> There is probably a better way to resolve this, but a possible solution is
> to be explicit with the namespace:
>
>
> GOnames=AnnotationDbi::select(GO.db,keys=pvals$category,columns=c("TERM","ONTOLOGY"))[,2:3]
>
> Cheers,
> Keith
>
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