[Bioc-devel] Problem with "RGChannelSetExtended" class form minfi

[Martin Morgan]

On 04/02/2017 05:15 AM, Mohammad Tanvir Ahamed via Bioc-devel wrote:
> Hi,
>
>
> In minfi (1.20.2), in current release version Bioconductor 3.4,  the "RGChannelSetExtended" class is defined as
>
>> getClass("RGChannelSetExtended")
>
> Class "RGChannelSetExtended" [package "minfi"]
>
> Slots:
>
> Name:       assayData          phenoData         featureData   experimentData  annotation        protocolData  .__classVersion__
> Class:       AssayData AnnotatedDataFrame  AnnotatedDataFrame            MIAxE   character  AnnotatedDataFrame          Versions
>
> Extends:
>
> Class "RGChannelSet", directly
> Class "eSet", by class "RGChannelSet", distance 2
> Class "VersionedBiobase", by class "RGChannelSet", distance 3
> Class "Versioned", by class "RGChannelSet", distance 4
>>
>
>
>
>
>
> But in minfi (1.21.5), in the development version Bioconductor 3.5, the "RGChannelSetExtended" class is defined as
>> getClass("RGChannelSetExtended")
>
> Class "RGChannelSetExtended" [package "minfi"]
>
> Slots:
>
> Name:  annotation     colData  assays             NAMES  elementMetadata  metadata
> Class:  character   DataFrame  Assays character_OR_NULL       DataFrame      list
>
> Extends:
> Class "RGChannelSet", directly
> Class "SummarizedExperiment", by class "RGChannelSet", distance 2
> Class "Vector", by class "RGChannelSet", distance 3
>
> Class "Annotated", by class "RGChannelSet", distance 4
>
>
> Now to make a new package, which class definition I need to use ?

Develop new packages using the 'devel' version of Bioconductor packages.

> And also , for dependency some other packages (wateRmelon, ChAMP), in their development version  Bioconductor 3.5, still using the old definition of "RGChannelSetExtended".

> If so, how to solve the problem ?

Somehow 'not your problem', the maintainers need to update their devel 
packages.

Martin

>
>
> Tanvir Ahamed
>
> Göteborg, Sweden  |  mashranga at yahoo.com
>
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