[Bioc-devel] BioC 3.0 CHECK ERROR
dtenenba at fredhutch.org
Wed Nov 26 19:03:52 CET 2014
----- Original Message -----
> From: "Martin Morgan" <mtmorgan at fredhutch.org>
> To: "Joachim Schumann" <joachim.schumann at ufz.de>, bioc-devel at r-project.org
> Sent: Wednesday, November 26, 2014 9:00:07 AM
> Subject: Re: [Bioc-devel] BioC 3.0 CHECK ERROR
> On 11/26/2014 01:39 AM, Joachim Schumann wrote:
> > Hi everyone,
> > this morning I got an email from bioconductor.
> > The message:
> > According to the "Build/check report" for BioC 3.0,
> > the flowCHIC package has the following problem(s):
> > ERROR for 'R CMD check' on zin1.
> > The error I get is the following:
> > Error in callGeneric() :
> > 'callGeneric' with a primitive needs explicit arguments (no
> > formal args defined)
> > Calls: calculate_overlaps_xor ... calculate_overlaps_xor -> .local
> > -> bXOR ->
> > round -> round -> callGeneric
> > Does anyone know what the problem is? It seems that the round
> > function causes
> > the error.
> This is some kind of interaction with Matrix
> > library(EBImage)
> > img = readImage(system.file(package="EBImage", "images",
> > "nuclei.tif"))
> > xx = round(img)
> > library(Matrix)
> > yy = round(img)
> Error in callGeneric() :
> 'callGeneric' with a primitive needs explicit arguments (no formal
> args defined)
> which defines a Math2 group generic. How long has this been
> appearing? It
> doesn't seem like the build system R, EBImage or Matrix has changed
> release, and the package is available via biocLite implying that it
> once built...
I think the build system R has changed since release, since it's running 3.1.2 which was released on 10/31/2014, but release was 10/14/2014.
Indeed, if I look at the flowCHIC_1.0.0.tgz DESCRIPTION file, I see in the "Built" line that it was built with R 3.1.1.
So this suggests a problem with R-3.1.2? Is this a bug we should report?
> > Best,
> > Joachim
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
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