R help - Aug 2007 - S4 methods: unable to find an inherited method

Hello all,

    I consider myself pretty new to the whole OO based programming so
I'm sorry if I'm doing something stupid.
> xml<-read.metlin(url)
Error in function (classes, fdef, mtable)  :
        unable to find an inherited method for function "read.metlin",
for signature "url"
>read.metlin
standardGeneric for "read.metlin" defined from package
".GlobalEnv"

function (xml, ...)
standardGeneric("read.metlin")
<environment: 0x83a8ae4>
Methods may be defined for arguments: xml
> url
                                       description
"http://metlin.scripps.edu/download/MSMS_test.XML"
                                             class
                                             "url"
                                              mode
                                               "r"
                                              text
                                            "text"
                                            opened
                                          "closed"
                                          can read
                                             "yes"
                                         can write
                                              "no"

I defined my methods as :


if (!isGeneric("read.metlin") )
    setGeneric("read.metlin", function(xml)
standardGeneric("read.metlin"))

setMethod("read.metlin", "xcmsRaw", function(xml) {
#Parsing the METLIN XML File
    reading<-readLines(xml)
#    do rest of script

})

Any help as to why I'm getting the inherited method error would be great.

Cheers,

Paul

Hi Paul,

"H. Paul Benton" <hpbenton at scripps.edu>
writes:
>     I consider myself pretty new to the whole OO based programming so
> I'm sorry if I'm doing something stupid.
These sorts of questions might be better sent to the R-devel list...
>> xml<-read.metlin(url)
> Error in function (classes, fdef, mtable)  :
>         unable to find an inherited method for function
"read.metlin",
> for signature "url"
So the error message is telling you that it can't find a method for
the read.metlin generic that matches the class of the xml argument you
passed in.

You defined:
> setMethod("read.metlin", "xcmsRaw", function(xml) {
> #Parsing the METLIN XML File
>     reading<-readLines(xml)
> #    do rest of script
>
> })
So there is a method for read.metlin when the xml argument is an
xcmsRaw object.  As you show, you passed in an object with class
"url".
>> url
>                                        description
> "http://metlin.scripps.edu/download/MSMS_test.XML"
>                                              class
>                                              "url"
> Any help as to why I'm getting the inherited method error would be
> great.
You either need to add a method specialized on the url class (warning,
url is not an S4 class, there will be tricks required).  Or you need
to pass in an xcmsRaw object.

Cheers,

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/