I have a stupidly simple function:

test = function(...) { table(...) }

If I just copy and paste this code into an R session and then run

test(Rle(1:10))

I get the expected result.  However, I'm trying to include this function as part of a package, after installing my package

mypackage::test(Rle(1:10))

I get

Error in as.vector(x, mode) : invalid 'mode' argument

Obviously this is not my actual function, but shows what my problem is.  I'm sure this is something to do with package namespace dependencies and if I put the right thing in DESCRIPTION and/or NAMESPACE it would work fine.  But I can't work out what I need to put where to make it work.

Really a question for the bioc-devel mailing list, but you need to figure out what functions, methods, and generics you're using

> Rle
standardGeneric for "Rle" defined from package "S4Vectors"

function (values = logical(0), lengths = integer(0)) 
standardGeneric("Rle")
<environment: 0x4e3c080>
Methods may be defined for arguments: values
Use  showMethods("Rle")  for currently available ones.
> methods(table)
[1] table,ANY-method       table,DataTable-method table,Rle-method      
[4] table,Vector-method   
see '?methods' for accessing help and source code
> environment(getMethod("table", "Rle"))
<environment: namespace:S4Vectors>

and add those to your NAMESPACE, e.g.,

importFrom(S4Vectors, Rle, table)

Some would suggest the simpler

import(S4Vectors)

which is easier to maintain but can lead to conflicts between identical symbols defined in different packages.