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