Dear all,

First, sorry for the double posting on the r-help and bioC, my mistake… Never meant to send it to the r-help list as it is a bioC question. So here it is…

I am writing a package with some of my favorite custom functions so that I can share them with others. I do not have a lot of experience building these packages and I apologize if this is a trivial question.

The issue I am having is with the generic function unlist used to unlist GRangesList object (unlist(GRL) from the IRanges package)

I have a function A in myPkg calling function B (myPkg::A{myPkg::B; …}), which is in the same package and call the unlist function of a GRangesList object (myPkg::B{ unlist(GRL); … }). For some reason, if I have the two function on the top level namespace, everything works, but when loaded from a package (library(myPkg); A(GRL)) it breaks at the unlist() step. However, if I fully qualify the unlist function in myPkgB (myPkg::B{IRanges::unlist(GRL); …} ), then calling A(GRL) after loading the myPkg library works.

So, are we expected to always fully qualify the unlist() function? (i.e. Calling it with it's package name myPkg::B{ IRanges::unlist(GRL) } ). I have been trying all strategy of Depends: and Imports: in my DESCRIPTION file and nothing works unless I fully qualify this function.

What is the best practice? I tried using only Imports: as suggested by Chambers but it breaks. Using Depends does not help.
Am I having clashing namespace? Here is my Depends: (or Imports:) line: Depends: Rsamtools, GenomicFeatures, parallel, rtracklayer, edgeR

Am I simply missing something?

Thanks

--  Marco Blanchette, Ph.D.
Stowers Institute for Medical Research
1000 East 50th Street
Kansas City MO 64110
www.stowers.org


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