On 07/13/2014 05:24 AM, Keith Hughitt wrote:
(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.hugh...@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
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
