[Bioc-devel] Unreproducible build check warning

Valerie Obenchain vobencha at fhcrc.org
Mon Mar 17 18:49:11 CET 2014

Hi Antti,

It's looking for


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,



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: vobencha at fhcrc.org
Phone:  (206) 667-3158
Fax:    (206) 667-1319

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