I'm in the process of converting some S3 methods to S4 methods.
I have this function :
setGeneric("enrichmentCalc", function(rs, organism, seqLen,
...){standardGeneric("enrichmentCalc")})
setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs,
organism, seqLen, ...) {
... ... ...
})
setMethod("enrichmentCalc", c("GenomeData", "BSgenome"), function(rs, organism,
seqLen=NULL, do.warn=FALSE) {
... ... ...
})
setMethod("enrichmentCalc", c("GRanges", "BSgenome"), function(rs, organism,
seqLen=NULL) {
... ... ...
}
and a part of my Rd file is :
\name{enrichmentCalc}
\docType{methods}
\alias{enrichmentCalc,GenomeDataList,BSgenome-method}
\alias{enrichmentCalc,GenomeData,BSgenome-method}
\alias{enrichmentCalc,GRanges,BSgenome-method}
... ... ...
\usage{
enrichmentCalc(rs, organism, seqLen, ...)
enrichmentCalc(rs, organism, seqLen=NULL, do.warn=FALSE)
enrichmentCalc(rs, organism, seqLen=NULL)
}
... ... ...
Can anyone suggest why I'm seeing this error :
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'enrichmentCalc':
enrichmentCalc
Code: function(rs, organism, seqLen, ...)
Docs: function(rs, organism, seqLen = NULL, do.warn = FALSE)
Argument names in code not in docs:
...
Argument names in docs not in code:
do.warn
Mismatches in argument names:
Position: 4 Code: ... Docs: do.warn
Mismatches in argument default values:
Name: 'seqLen' Code: Docs: NULL
enrichmentCalc
Code: function(rs, organism, seqLen, ...)
Docs: function(rs, organism, seqLen = NULL)
Argument names in code not in docs:
...
Mismatches in argument default values:
Name: 'seqLen' Code: Docs: NULL
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'enrichmentCalc':
enrichmentCalc
Also, what is the difference between
... ... ...
\docType{methods}
... ... ...
\alias{methodName,class-method}
... ... ...
\usage{methodName(arg1)}
... ... ...
and
... ... ...
\alias{methodName,class-method}
... ... ...
\usage
{
\S4method{methodName}{class}(arg1)
}
... ... ...
I've seen both ways used for S4 methods and don't know what is the underlying
difference.
I haven't been able to find any good tutorials for the new S4 architecture
(written post 2006), so I'm not sure where to start with S4.
Thanks,
Dario.
--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
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