Date: Thu, 26 Jun 2014 04:00:11 +0000
From: Dario Strbenac <dstr7...@uni.sydney.edu.au>
To: "bioc-devel@r-project.org" <bioc-devel@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
------------------------------
______________________________________________________________________
The information in this email is confidential and intend...{{dropped:4}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
