Entering edit mode
Hi, in my package I have a method which subsets a DNAStringSet:
setGeneric("subsetSites",
function(object, index){
standardGeneric("subsetSites")
}
)
setMethod("subsetSites",
signature("DNAStringSet", "integer"),
function(object, index){
index <- rep.int(list(index), length(object))
return(object[index])
}
)
This works in a script with Biostrings and IRanges:
library(Biostrings)
library(IRanges)
setGeneric("subsetSites",
function(object, index){
standardGeneric("subsetSites")
}
)
setMethod("subsetSites",
signature("DNAStringSet", "integer"),
function(object, index){
index <- rep.int(list(index), length(object))
return(object[index])
}
)
dna <-
DNAStringSet(readDNAMultipleAlignment(filepath =
system.file("extdata",
"msx2_mRNA.aln",
package="Biostrings"),
format="clustal"))
sub <- subsetSites(dna, 1:50)
However, when subsetSites is a non-exported functions for internal use in my package it does not work - even when Biostrings and IRanges are imported, and so stuff in their namespaces should be "visible" to the package namespace:
Error in end(PartitioningByEnd(x)) : error in evaluating the argument 'x' in selecting a method for function 'end': Error: could not find function "PartitioningByEnd"
This is confusing since PartitioningByEnd looks like it is exported from IRanges. I have import(Biostrings)
and import(IRanges) in my namespace file.
Imports:
Biostrings,IRanges
Is in the description file.
Thanks,
Ben.
