[Bioc-devel] BioC 3.0 CHECK ERROR

[Joachim Schumann]

Thanks for all the answers. I corrected the code. The problem was that round() does not work on an Image object of EBImage as it did before.
In the package I could call round(Image,digits=3) but now it only works using round(Image at .Data,digits=3).
I will fix this.

Joachim

Am 27/11/14 08:05 schrieb Martin Morgan  <mtmorgan at fredhutch.org>:
> 
> On 11/26/2014 07:36 PM, Dan Tenenbaum wrote:
> >
> >
> >----- Original Message -----
> >>From: "Martin Morgan" <mtmorgan at fredhutch.org>
> >>To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> >>Cc: "Joachim Schumann" <joachim.schumann at ufz.de>, bioc-devel at r-project.org
> >>Sent: Wednesday, November 26, 2014 5:33:22 PM
> >>Subject: Re: [Bioc-devel] BioC 3.0 CHECK ERROR
> >>
> >>On 11/26/2014 10:03 AM, Dan Tenenbaum wrote:
> >>>
> >>>
> >>>----- 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?
> >>
> >>The path to Matrix is
> >>
> >>flowCHIC
> >> Imports: vegan
> >> Imports: mgcv
> >> Imports: Matrix
> >>
> >>vegan was updated on
> >>
> >> > packageDescription("vegan")[c('Version', 'Date/Publication')]
> >>$Version
> >>[1] "2.2-0"
> >>
> >>$`Date/Publication`
> >>[1] "2014-11-17 11:35:34"
> >>
> >>and changed (based on comparison with the last archived version,
> >>2.0-10 from
> >>http://cran.fhcrc.org/src/contrib/Archive/vegan) to move Matrix from
> >>Suggests:
> >>to Imports:.
> >>
> >>I think it's a long-standing issue in R; I can reproduce it using the
> >>EBImage /
> >>Matrix example in R 2.15, for instance (although oddly I had to go
> >>through some
> >>mild histrionics to get EBImage to compile). Specifically, it seems
> >>like a patch
> >>that Michael just applied in R-devel (!), plus
> >>
> >>Index: MethodsListClass.R
> >>===================================================================
> >>--- MethodsListClass.R	(revision 67060)
> >>+++ MethodsListClass.R	(working copy)
> >>@@ -353,7 +353,7 @@
> >> function(x, digits) {
> >> value <- x
> >> x <- x at .Data
> >>- value at Data <- callGeneric()
> >>+ value at .Data <- callGeneric()
> >> value
> >> })
> >> ## some methods for nonStructure, ensuring that the class and
> >> slots
> >>
> >>
> >
> >Are you going to commit this? If this (and Michael's change) fixes the problem, then I will update the build machines. BTW flowCHIC has the same issue in release, so I guess some backporting is in order.
> >
> 
> Both R-devel and R-3-1-branch will have a fix.
> 
> For flowCHIC, I'd leave devel as-is, it will eventually heal itself.
> 
> For release, I think Joachim should explore an alternative so that users of the current R release can use flowCHIC without waiting for the next release in the R-3-1 series. I'm not really familiar with the EBImage package, but I think what you want to do is the equivalent of
> 
>  x = initialize(x, round(imageData(x) * (2^8 - 1), digits = 3))
> 
> i.e., calculating round() on the raw array, then updating the Image object 'x'.
> 
> Martin
> 
> >Dan
> >
> >
> >>Martin
> >>
> >>>
> >>>Dan
> >>>
> >>>
> >>>>
> >>>>Martin
> >>>>
> >>>>>
> >>>>>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
> >>>>
> >>>>_______________________________________________
> >>>>Bioc-devel at r-project.org mailing list
> >>>>https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>
> >>
> >>
> >>--
> >>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
> >>
> 
> 
> -- 
> 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
> 
-- 

Joachim Schumann
Department of Environmental Microbiology
AG Flow Cytometry
Helmholtz Centre for Environmental Research - UFZ
Permoserstraße 15, 04318 Leipzig

E-Mail: joachim.schumann at ufz.de 
http://www.ufz.de

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