[BioC] IRanges::unlist in package

[Hervé Pagès]

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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>>> Bioconductor at r-project.org
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>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>> --
>> 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
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