Thomas, If I delete the \seealso section, I still get the same strange behavior. Shouldn't removing that line fix the problem?
Thanks, Steve -----Original Message----- From: Thomas Lumley [mailto:[EMAIL PROTECTED] Sent: Tuesday, April 04, 2006 10:13 AM To: Steven Lacey Cc: [email protected] Subject: Re: [R] documenting s4 methods in package On Tue, 4 Apr 2006, Steven Lacey wrote: > 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? No. It means that you still have \link{~~fun~~} in the \seealso section. -thomas > 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=FAL > SE){st > andardGeneric("getRemovedDf.OAD")}) > > setMethod("getRemovedDf.OAD","status.or.rm.v1", > function(x,y,z,simplify,descrip){ > if(length(0">[EMAIL PROTECTED]) <mailto:[EMAIL PROTECTED])> >0){ > pred <- unlist(lapply([EMAIL PROTECTED],function(x)x[1])) > resp <- unlist(lapply([EMAIL PROTECTED],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([EMAIL PROTECTED],function(x)length([EMAIL > PROTECTED]))) > if(all(i==0)){ > return(list()) > } else { > if(simplify) [EMAIL PROTECTED](along=i)[i==0]] > <mailto:[EMAIL PROTECTED](along=i)[i==0]]<-NULL> <-NULL > tmp <- > lapply([EMAIL PROTECTED],getRemovedDf.OAD,[EMAIL PROTECTED],[EMAIL PROTECTED]) > if(descrip){ > f <- as.data.frame(descrip[!"history"%in%names([EMAIL > PROTECTED])]) > 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("getRemove > dDf.OA > D")} > } > \keyword{ ~kwd1 }% at least one, from doc/KEYWORDS > \keyword{ ~kwd2 }% __ONLY ONE__ keyword per line > > > [[alternative HTML version deleted]] > > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
