From bodenhofer at bioinf.jku.at  Fri Dec 14 09:46:43 2012
From: bodenhofer at bioinf.jku.at (Ulrich Bodenhofer)
Date: Fri, 14 Dec 2012 09:46:43 +0100
Subject: [Rd] Strange, most probably unjustified,
 codoc mismatch for S4 method with one argument plus '...' (re-try)
Message-ID: <50CAE773.8070004@bioinf.jku.at>

Hi,

I just figured out that I accidentally posted my message in HTML, so I 
am retrying in plain text only. Sorry.

I am currently extending one of our CRAN packages and ran into an 
unexpected problem when checking the source package. I got some warnings 
in the step "* checking for code/documentation mismatches". I double 
checked everything and did not see anything that would actually justify 
this warning. After testing around for quite a while, I think I can now 
pinpoint the problem. In order to make myself clear, I need to explain 
the situation in more detail:

The default method (passed as def argument of setGeneric()) has the 
formal argument list (x, y, ...). Suppose I want to register a method 
with a signature without y, say signature(x="matrix", y="missing"). If I 
pass a function to setMethod() that only has the argument x,i.e. 
function(x) {...}, everything works well. It also works well if I 
register a function with additional arguments, e.g. function(x, 
dummy=NULL, ...){...} (note: y is missing in the definition). However, 
if I try to register a function with two formal arguments, x and '...', 
i.e.function(x, ...){...}, I get the warning that argument y is present 
in the code but missing in the documentation , although it is actually 
NOT in the code. In order to make this reproducible for everybody, I put 
together a little dummy package in which one of the methods leads to 
exactly this warning:

    http://www.bioinf.jku.at/people/bodenhofer/codocMismatchTest_0.0.1.tar.gz

Just run 'R CMD check' on this archive and you'll see. You will also see 
from the code and the corresponding documentation that the warning seems 
unjustified. I tried the following R versions: 2.12.1, 2.13.0, 2.13.1, 
2.14.0, 2.14.1, 2.15.0, 2.15.1, 2.15.2, 2.16.0 (devel), and all 
consistently gave the same warning.

Is this a bug or is there a special reason for this behavior? Any help 
is gratefully appreciated!

Thanks in advance and best regards,
Ulrich


------------------------------------------------------------------------
*Dr. Ulrich Bodenhofer*
Associate Professor
Institute of Bioinformatics

*Johannes Kepler University*
Altenberger Str. 69
4040 Linz, Austria

Tel. +43 732 2468 4526
Fax +43 732 2468 4539
bodenhofer at bioinf.jku.at <mailto:bodenhofer at bioinf.jku.at>
http://www.bioinf.jku.at/ <http://www.bioinf.jku.at>



[Rd] Strange, most probably unjustified, codoc mismatch for S4 method with one argument plus '...' (re-try)
Ulrich Bodenhofer