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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