[BioC] IRanges::unlist in package

[Blanchette, Marco]

Thanks Herve, seems like this solves all my issues. 

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Marco Blanchette, Ph.D.
Genomic Scientist
Stowers Institute for Medical Research
1000 East 50th St.
Kansas City, MO 64110

Tel: 816-926-4071 
Cell: 816-726-8419 
Fax: 816-926-2018

On Aug 12, 2013, at 2:16 PM, "Hervé Pagès" <hpages at fhcrc.org> wrote:

> Hi,
> 
> On 08/12/2013 09:01 AM, Blanchette, Marco wrote:
>> Thanks James, yep, importMethodsFrom() did the trick for that function.
>> Now, I am stuck with a second function that also breaks when deployed from
>> a package but works just fine when located in the top level namespace. The
>> problem with this one is that it does not break per se but returns NA's,
>> which makes locating the faulty step quite difficult to find!
>> 
>> So, I have two questions:
>> 1) What's the best strategy to identify the packages that needs to have
>> their methods imported by the importMethodsFrom() function
>> 2) What is the best way to debug functions that behave differently when
>> loaded in a package vs on top level. Is there a way to "step in" a given
>> namespaceŠ
> 
> If your package operates on GRanges and GRangesList objects, I would
> highly recommend you put BiocGenerics, IRanges, and GenomicRanges in
> your Depends field, and that you also import them entirely in your
> NAMESPACE:
> 
> import(BiocGenerics)
> import(IRanges)
> import(GenomicRanges)
> 
> That will avoid you a lot of headaches (and also no need to fully
> qualify function names).
> 
> Cheers,
> H.
> 
>> 
>> Thanks
>> 
>> 
>> --  Marco Blanchette, Ph.D.
>> Stowers Institute for Medical Research
>> 1000 East 50th Street
>> Kansas City MO 64110
>> www.stowers.org
>> 
>> 
>> 
>> 
>> 
>> 
>> On 8/7/13 4:09 PM, "James W. MacDonald" <jmacdon at uw.edu> wrote:
>> 
>>> Hi Marco,
>>> 
>>> On 8/7/2013 4:51 PM, Blanchette, Marco wrote:
>>>> Dear all,
>>>> 
>>>> First, sorry for the double posting on the r-help and bioC, my mistakeŠ
>>>> Never meant to send it to the r-help list as it is a bioC question. So
>>>> here it isŠ
>>>> 
>>>> 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;
>>>> Š}), which is in the same package and call the unlist function of a
>>>> GRangesList object (myPkg::B{ unlist(GRL); Š }). 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); Š} ), 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.
>>> 
>>> I don't think you want to depend on IRanges if you only use this one
>>> function. Instead, you should be adding IRanges to the Imports list in
>>> your DEPENDS file, and using a NAMESPACE file that includes
>>> 
>>> importMethodsFrom(IRanges, unlist)
>>> 
>>> See
>>> 
>>> http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Namespaces-wit
>>> h-S4-classes-and-methods
>>> 
>>> for more information.
>>> 
>>> Best,
>>> 
>>> Jim
>>> 
>>> 
>>>> 
>>>> 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
>>>> 
>>>> 
>>>>    [[alternative HTML version deleted]]
>>>> 
>>>> 
>>>> 
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>>> 
>>> --
>>> James W. MacDonald, M.S.
>>> Biostatistician
>>> University of Washington
>>> Environmental and Occupational Health Sciences
>>> 4225 Roosevelt Way NE, # 100
>>> Seattle WA 98105-6099
>> 
>> _______________________________________________
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> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319