On 4/4/2006 1:58 PM, Steven Lacey wrote: > Thomas, > > Correction! If I remove the \seealso line the missing ~~fun~~ disppears > (thank you!), but now "chm" appears at the end of the line decribing the > help page building. Most lines do not have that, only "text htm1 latex > example". What does the chm signify and how does one get rid of it?
"chm" indicates that you have built a compiled HTML version of your man page. It will be shown in Windows if you ask for help after options(chmhelp=TRUE). You can edit the MkRules file to disable production of this kind of help page. Duncan Murdoch > > Thanks, > Steve > > -----Original Message----- > From: Steven Lacey [mailto:[EMAIL PROTECTED] > Sent: Tuesday, April 04, 2006 1:54 PM > To: 'Thomas Lumley' > Cc: 'r-help@stat.math.ethz.ch' > Subject: RE: [R] documenting s4 methods in package > > > 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: r-help@stat.math.ethz.ch > 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]] >> >> ______________________________________________ >> R-help@stat.math.ethz.ch 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 > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html