[Bioc-devel] edgeR estimateGLMRobustDisp Fails when Called From A Package

[Gordon K Smyth]

> Date: Thu, 26 Jun 2014 04:00:11 +0000
> From: Dario Strbenac <dstr7320 at uni.sydney.edu.au>
> To: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
> Subject: [Bioc-devel] edgeR estimateGLMRobustDisp Fails when Called
> 	From A	Package
>
> Hello,
>
> I am writing a package that has a function that uses estimateGLMRobustDisp, leading to an error :
>
> Error in dispBinTrend(y, design, offset = offset, method.trend = "loess",  :
>  could not find function "loessFit"
> Calls: edgeRselection ... estimateGLMTrendedDisp -> estimateGLMTrendedDisp.default -> dispBinTrend
>
> I import estimateGLMRobustDisp from edgeR in my NAMESPACE file. This 
> error is because edgeR depends on limma, rather than importing from it. 
> I want to avoid using parent.env<- and .onLoad to get around the 
> problem. Is there any hope of modifying the edgeR description file to 
> have limma in the Imports field ?

Nope, because that is neither necessary nor good programming practice 
(according to R core).

I will however add loessFit to importFrom() in edgeR's NAMESPACE, which I 
think will solve your problem.

Best wishes
Gordon

> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
>
> ------------------------------

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