Hi Antti,
It's looking for
\alias{[,scoreList,ANY-method}
The generic '[' can dispatch on arguments 'x', 'i' and 'j'.
getGeneric("[")
standardGeneric for "[" defined from package "base"
function (x, i, j, ..., drop = TRUE)
standardGeneric("[", .Primitive("["))
<bytecode: 0x237af30>
<environment: 0x21d9f18>
Methods may be defined for arguments: x, i, j, drop
Use showMethods("[") for currently available ones.
The method you wrote for scoreList dispataches on 'x' as a scoreList
object but doesn't specify 'i' or 'j'. One of these indices must be
present in order for subsetting to happen. In this case (I believe) the
default is assuming 'i' as ANY and 'j' as missing.
For example, with the VCF class I've specified the method for ANY, ANY:
setMethod("[", c("VCF", "ANY", "ANY"),
function(x, i, j, ..., drop=TRUE)
{
...
To see more examples,
showMethods('[')
Valerie
On 03/17/2014 08:13 AM, Antti Honkela wrote:
Hi all,
The latest build check report shows one warning for 'tigre':
---------------------------------------
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'scoreList,ANY'
---------------------------------------
As far as I can tell the method in question should be documented, as one
of the .Rd files contains an alias:
\alias{[,scoreList-method}
Furthermore I cannot reproduce it on my own using the latest R-alpha (or
R-devel from last week): R CMD check on the source tar-ball downloaded
directly from Bioconductor runs cleanly.
Can someone please help in figuring out what is going on?
Antti
--
Valerie Obenchain
Program in Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B155
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: voben...@fhcrc.org
Phone: (206) 667-3158
Fax: (206) 667-1319
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