[Bioc-devel] BioC 3.0 CHECK ERROR

----- 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

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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


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] BioC 3.0 CHECK ERROR

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