[Bioc-devel] class name collision in cache: igvR and Gviz

Hervé Pagès hpages at fredhutch.org
Fri May 4 20:30:09 CEST 2018

Hi Paul,

Luckily you caught this only 3 days after the release so renaming the
class now is probably ok and shouldn't be disruptive.


On 05/04/2018 10:52 AM, Paul Shannon wrote:
> I just discovered a class name collision - AnnotationTrack, in Gviz and my new package igvR.   wish to get wise counsel before proceeding with a fix.  Here’s the error message:
>     Found more than one class "AnnotationTrack" in cache;
>     using the first, from namespace ‘igvR' Also defined by ‘Gviz’
> AnnotationTrack is an abstract base class in my new package igvR.  The concrete derived classes at present are
>    DataFrameAnnotationTrack
>    GRangesAnnotationTrack
>    UCSCBedAnnotationTrack
> It would be easy for me to rename AnnotationTrack to “GenomeAnnotationTrack” or even “igvAnnotationTrack”, thereby  avoiding the name clash.
> Reasonable?  Fix in both release and devel?
> Thanks -
>   - Paul
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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