[Bioc-devel] BioC 3.0 CHECK ERROR

----- 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

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PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793

[Bioc-devel] BioC 3.0 CHECK ERROR

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