Hi, 
 
I have written a package that contains many s4 generic functions and
associated methods. I am having a lot of trouble getting R to build the help
pages for these generic functions without reporting, "missing link(s):
~~fun~~, which means that it cannot find the appropriate function when code
in the example section of the help is run. Right?
 
After some playing around I can get it to build the help without missing a
link, but often I am not sure what I have done to correct the "problem" and
it takes a lot of time. 
 
For instance, I had the package build the help without missing a function
link. I then added a argument to two different functions and updated the
corresponding .rd help files and now when R build the help pages it reports
"missing link(s):  ~~fun~~. What is going on?
 
Below is the code from the help file and the associated s4 method. 
 
Any help would be greatly appreciated. 
 
Steve
 
GENERIC FUNCTION AND METHODS
 
setGeneric("getRemovedDf.OAD",function(x,y,z,simplify=TRUE,descrip=FALSE){st
andardGeneric("getRemovedDf.OAD")})
 
setMethod("getRemovedDf.OAD","status.or.rm.v1",
    function(x,y,z,simplify,descrip){
        if(length(0">x@removed) <mailto:x@removed)> >0){
            pred <- unlist(lapply(x@removed,function(x)x[1]))
            resp <- unlist(lapply(x@removed,function(x)x[2]))
            out  <- data.frame(pred,resp)
            names(out) <- c(y,z)
            return(out)
        } else {
            return(data.frame())
        }
    }
)
    
setMethod("getRemovedDf.OAD","sa",
    function(x,y,z,simplify,descrip){
        i <- unlist(lapply(x@outlier.removal,function(x)length(x@removed)))
        if(all(i==0)){
            return(list())
        } else {
            if(simplify) x@outlier.removal[seq(along=i)[i==0]]
<mailto:x@outlier.removal[seq(along=i)[i==0]]<-NULL> <-NULL    
            tmp <-
lapply(x@outlier.removal,getRemovedDf.OAD,x@predictorName,x@responseName)
            if(descrip){
                f <- as.data.frame(descrip[!"history"%in%names(x@descrip)])
                return(lapply(tmp,function(x)cbind(f,x)))
            } else {
                return(tmp)
            }
        }
    }
)

 
MAN FILE
\name{getRemovedDf.OAD}
\alias{getRemovedDf.OAD}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ ~~function to do ... ~~ }
\description{
  ~~ A concise (1-5 lines) description of what the function does. ~~
}
\usage{
getRemovedDf.OAD(x, y, z, simplify = TRUE, descrip=FALSE)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{x}{ ~~Describe \code{x} here~~ }
  \item{y}{ ~~Describe \code{y} here~~ }
  \item{z}{ ~~Describe \code{z} here~~ }
  \item{simplify}{ ~~Describe \code{simplify} here~~ }
  \item{descrip}{ ~~Describe \code{descrip} here~~ }  
}
\details{
  ~~ If necessary, more details than the __description__  above ~~
}
\value{
  ~Describe the value returned
  If it is a LIST, use
  \item{comp1 }{Description of 'comp1'}
  \item{comp2 }{Description of 'comp2'}
  ...
}
\references{ ~put references to the literature/web site here ~ }
\author{ ~~who you are~~ }
\note{ ~~further notes~~ }
 
 ~Make other sections like Warning with \section{Warning }{....} ~
 
\seealso{ ~~objects to See Also as \code{\link{~~fun~~}}, ~~~ }
\examples{
##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--    or do  help(data=index)  for the standard data sets.
 
## The function is currently defined as
function(x,y,z,simplify=TRUE,descrip=FALSE){standardGeneric("getRemovedDf.OA
D")}
}
\keyword{ ~kwd1 }% at least one, from doc/KEYWORDS
\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line


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