Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'

[drisso]

This message has been annoying us for a long time.

I'm opening an issue because I found where it comes from. The problem is that the class "Annotated" is defined both in the S4Vectors package (a dependency of SummarizedExperiment) and in the RNeXML package (a dependency of phylobase). Note that we want the former.

This is a minimal example that illustrates the behavior:

library(SummarizedExperiment)
SummarizedExperiment()
# class: SummarizedExperiment 
# dim: 0 0 
# metadata(0):
# assays(0):
# rownames: NULL
# rowData names(0):
# colnames: NULL
# colData names(0):
library(RNeXML)
SummarizedExperiment()
# Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
# class: SummarizedExperiment 
# dim: 0 0 
# metadata(0):
# assays(0):
# rownames: NULL
# rowData names(0):
# colnames: NULL
# colData names(0):

Since we need to import both packages, I don't see any obvious way to make this disappear. Emailing the Bioc devel mailing list might be a good idea. It may be something that needs to be fixed in SummarizedExperiment, since we are not directly using the Annotated class.