[Rd] smoothScatter() and the KernSmooth package

davide risso risso.davide at gmail.com
Wed Feb 18 21:19:33 CET 2015

Dear R-devel,

my Bioconductor EDASeq package has a function MDPlot that uses the
smoothScatter() function from the graphics package. When I test this
package on travis-ci.org (R CMD check) I get the following error
(which I don't get on my machine nor on the Bioconductor build

* checking examples ... ERROR
Running examples in ‘EDASeq-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MDPlot-methods
> ### Title: Methods for Function 'MDPlot' in Package 'EDASeq'
> ### Aliases: MDPlot MDPlot-methods MDPlot,matrix,numeric-method
> ###   MDPlot,SeqExpressionSet,numeric-method
> ### Keywords: methods
> ### ** Examples
> library(yeastRNASeq)
> data(geneLevelData)
> data(yeastGC)
> sub <- intersect(rownames(geneLevelData), names(yeastGC))
> mat <- as.matrix(geneLevelData[sub,])
> data <- newSeqExpressionSet(mat,
+             phenoData=AnnotatedDataFrame(
+                       data.frame(conditions=factor(c("mut", "mut",
"wt", "wt")),
+                                  row.names=colnames(geneLevelData))),
+             featureData=AnnotatedDataFrame(data.frame(gc=yeastGC[sub])))
> MDPlot(data,c(1,3))
Error in loadNamespace(name) : there is no package called ‘KernSmooth’
Calls: MDPlot ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

I looked at the code in smoothScatter and there is a call to
grDevices:::.smoothScatterCalcDensity(), which in turn calls

This gets fixed by adding KernSmooth as suggested package in EDASeq.

I was able to reproduce this issue (and the fix) in a small R package:

I have a few questions: isn't it unusual the way smoothScatter calls
grDevices:::.smoothScatterCalcDensity() and KernSmooth::bkde2D(),
i.e., without requiring the packages?
Shouldn't "graphics" suggest "KernSmooth"?

Best regards,

Davide Risso, PhD
Post Doctoral Scholar
Division of Biostatistics
School of Public Health
University of California, Berkeley
344 Li Ka Shing Center, #3370
Berkeley, CA 94720-3370
E-mail: davide.risso at berkeley.edu

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