[Bioc-devel] BioC 3.0 CHECK ERROR

[Dan Tenenbaum]

----- 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.

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
>