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 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.