[R] chippeakanno package: "getAllPeakSequence" problem

Martin Morgan mtmorgan at fhcrc.org
Wed Sep 21 17:20:29 CEST 2011

On 09/21/2011 08:08 AM, Nico902 wrote:
> Hi all,
> I am using the package ChIPpeakAnno, and I have a problem with the function
> getAllPeakSequence. This is related to object oriented programming I think,
> I have the following message:
>> peaksWithSequences<- getAllPeakSequence(peakList, upstream = 100,
>> downstream = 100, genome = Hsapiens)
> Error in validObject(.Object) :
>    invalid class "GRanges" object: superclass "Sequence" not defined in the
> environment of the object's class
> Is the error coming from my configuration or from the code? I do not know
> many things about OOP in R.

Hi Nico902

Please ask questions about this Bioconductor package on the Bioconductor 
mailing list.


Likely your packages are not at a consistent version. Follow these 


to update your packages.


> Thanks.
> --
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> Sent from the R help mailing list archive at Nabble.com.
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