[Bioc-devel] BioC 3.0 CHECK ERROR

[Martin Morgan]

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


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
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>>


-- 
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