[Bioc-devel] BioC 3.0 CHECK ERROR

[Dan Tenenbaum]

----- 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
> since
> 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?

Dan


> 
> Martin
> 
> >
> > Best,
> > Joachim
> >
> 
> 
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