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

(patch with above change...)

it's better to amend the NAMESPACE to include

   importFrom(AnnotationDbi, select)

The codetoolsBioC package (available from the Bioconductor svn repository) 
suggests (this is not completely reliable) that there might be other namaespace 
import issues. (some would argue for less selective import, because the code is 
then easier to maintain, e.g., import(BiocGenerics), etc).

 > codetoolsBioC::writeNamespaceImports("goseq")
#Generated by codetoolsBioC version 0.0.23
#Timestamp: Sun Jul 13 05:29:07 2014

#Imports: AnnotationDbi, BiasedUrn, BiocGenerics, DBI, geneLenDataBase,
#         GenomeInfoDb, GO.db, graphics, IRanges, methods, mgcv,
#         S4Vectors, stats, utils

importMethodsFrom(AnnotationDbi, select, toTable)

importMethodsFrom(BiocGenerics, as.data.frame, as.vector, cbind,
                   colnames, "colnames<-", get, lapply, mapply, match,
                   ncol, nrow, order, paste, rbind, rownames,
                   "rownames<-", sapply, sort, table, unique, unlist)

importMethodsFrom(DBI, summary)

importMethodsFrom(GenomeInfoDb, "genome<-")

importMethodsFrom(IRanges, gsub, mean, split, tolower, which)

importMethodsFrom(methods, show)

importMethodsFrom(S4Vectors, "%in%", t)

importFrom(BiasedUrn, dWNCHypergeo, pWNCHypergeo)

importFrom(geneLenDataBase, unfactor)

importFrom(graphics, lines, plot)

importFrom(mgcv, gam, mono.con, pcls, Predict.matrix, s, smoothCon)

importFrom(stats, approx, binomial, dhyper, median, phyper, runif)

importFrom(utils, relist)

importFrom(GO.db, GO.db)

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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