On 12/14/2012 09:46 AM, Ulrich Bodenhofer wrote:
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!
In ?setMethod there is this paragraph
It is possible to have some differences between the formal
arguments to a method supplied to 'setMethod' and those of the
generic. Roughly, if the generic has ... as one of its arguments,
then the method may have extra formal arguments, which will be
matched from the arguments matching ... in the call to 'f'. (What
and in practice the expectation is that if a generic has formals x, y, and ...,
then a method will have formals x, y, and possibly additional arguments. None of
these methods follow this
setMethod("dummyMethod", signature(x="matrix", y="missing"),
function(x) {})
setMethod("dummyMethod", signature(x="matrix", y="missing"),
function(x) {})
setMethod("dummyMethod", signature(x="data.frame", y="missing"),
function(x, ...) {})
each should have been written as, for instance
setMethod("dummyMethod", signature(x="matrix", y="missing"),
function(x, y, ...) {})
The reason for the codoc warning stems from how R represents methods with
signatures different from their generic, typically when _additional_ arguments
are used,
(what
actually happens is that a local function is created inside the
method, with the modified formal arguments, and the method is
re-defined to call that local function.)
So e.g.,
selectMethod(dummyMethod, c("matrix", "missing"))
Method Definition:
function (x, y, ...)
{
.local <- function (x)
{
}
.local(x, ...)
}
Signatures:
x y
target "matrix" "missing"
defined "matrix" "missing"
and hence the codoc warning
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'dummyMethod':
\S4method{dummyMethod}{data.frame,missing}
Code: function(x, y, ...)
Docs: function(x, ...)
Argument names in code not in docs:
y
Mismatches in argument names:
Position: 2 Code: y Docs: ...
Your other setMethod
also results in code that likely differs from your expectation, e.g., no
argument matching by position
setMethod("dummyMethod", signature(x="list", y="missing"),
function(x, sel=NULL, ...) {})
> selectMethod(dummyMethod, signature(x="list", y="missing"))
Method Definition:
function (x, y, ...)
{
.local <- function (x, sel = NULL, ...)
{
}
.local(x, ...)
}
Signatures:
x y
target "list" "missing"
defined "list" "missing"
Hope that helps,
Martin
>
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
bodenho...@bioinf.jku.at <mailto:bodenho...@bioinf.jku.at>
http://www.bioinf.jku.at/ <http://www.bioinf.jku.at>
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