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Steven Lacey

2006-Apr-04 13:22 UTC

[R] documenting s4 methods in package

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


	[[alternative HTML version deleted]]

Thomas Lumley

2006-Apr-04 14:13 UTC

head link

[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=FALSE){st
> andardGeneric("getRemovedDf.OAD")})
>
> setMethod("getRemovedDf.OAD","status.or.rm.v1",
>    function(x,y,z,simplify,descrip){
>        if(length(0">x at removed) <mailto:x at removed)>
>0){
>            pred <- unlist(lapply(x at removed,function(x)x[1]))
>            resp <- unlist(lapply(x at 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 at outlier.removal,function(x)length(x at
removed)))
>        if(all(i==0)){
>            return(list())
>        } else {
>            if(simplify) x at outlier.removal[seq(along=i)[i==0]]
> <mailto:x at outlier.removal[seq(along=i)[i==0]]<-NULL> <-NULL
>            tmp <-
> lapply(x at outlier.removal,getRemovedDf.OAD,x at predictorName,x at
responseName)
>            if(descrip){
>                f <-
as.data.frame(descrip[!"history"%in%names(x at 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
>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at 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
tlumley at u.washington.edu	University of Washington, Seattle

Steven Lacey

2006-Apr-04 17:58 UTC

head link

[R] documenting s4 methods in package

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?

Thanks,
Steve 

-----Original Message-----
From: Steven Lacey [mailto:slacey at umich.edu] 
Sent: Tuesday, April 04, 2006 1:54 PM
To: 'Thomas Lumley'
Cc: 'r-help at 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:tlumley at u.washington.edu] 
Sent: Tuesday, April 04, 2006 10:13 AM
To: Steven Lacey
Cc: r-help at 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">x at removed) <mailto:x at removed)>
>0){
>            pred <- unlist(lapply(x at removed,function(x)x[1]))
>            resp <- unlist(lapply(x at 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 at outlier.removal,function(x)length(x at
removed)))
>        if(all(i==0)){
>            return(list())
>        } else {
>            if(simplify) x at outlier.removal[seq(along=i)[i==0]]
> <mailto:x at outlier.removal[seq(along=i)[i==0]]<-NULL> <-NULL
>            tmp <-
> lapply(x at outlier.removal,getRemovedDf.OAD,x at predictorName,x at
responseName)
>            if(descrip){
>                f <-
as.data.frame(descrip[!"history"%in%names(x at 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("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 at 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
tlumley at u.washington.edu	University of Washington, Seattle

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