Dear all,
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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