R CMD check WARNING \usage question

I'm trying to update a package and would like to crush a WARNING message for a clean build. 

I've been struggling with this question and haven't gotten any traction on the web either.

I've got a document file (Rd) that contains the following \usage statement:

\name{sample.data}
\alias{sample.data}

\title{CONIFERS forest growth model sample data}

\description{ A list object of type \code{sample.data} stores all of
the basic information about a \code{\link{data.frame}} object
representing a sample of plants.}

\usage{
x <- list( plots=data.frame(), plants=data.frame(), age=0, x0=0.0, n.years.projected=0 )
class(x)  <- "sample.data"
}

When I run R CMD check [pkg], I get the following WARNING:

* checking Rd \usage sections ... WARNING
Assignments in \usage in documentation object 'sample.data':
 x <- list(plots, plants, age = 0, x0 = 0, n.years.projected = 0)
 class(x) <- "sample.data"

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd contents ... OK

I'm not sure if there's a problem with the \alias section or the \usage section or both sections (I'm assuming this is the case).

I've read the Chapter 2 of R-ext.pdf plenty and just can't seem to see where I'm blowing it.

Respectfully,
Jeff.


Jeff Hamann, PhD
PO Box 1421
Corvallis, Oregon 97339-1421
541-754-2457
jeff.hamann[at]forestinformatics[dot]com
jeff.d.hamann[at]gmail[dot]com
http://www.forestinformatics.com
http://en.wikipedia.org/wiki/Forest_informatics

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I know I should provide a better answer, but I think it's really for a function.

For this package, we simply pass a list object about, but have to obfuscate it using a domain familiar nomenclature for the users.

So, not a data set, but a function. I think.

Here's the file in it's entirety:


%%	$Id $	

\name{sample.data}
\alias{sample.data}

\title{CONIFERS forest growth model sample data}

\description{ A list object of type \code{sample.data} stores all of
the basic information about a \code{\link{data.frame}} object
representing a sample of plants.}

\usage{
x<- list( plots=data.frame(), plants=data.frame(), age=0, x0=0.0, n.years.projected=0 )
class(x)<- "sample.data"
}

\details{
	To create the basic data type used in rconifers, you create a
	list object with the following elements (order is not
	important):
\describe{
\item{plots}{is a \link{data.frame} with the the same elements as \code{\link{plots.swo}}.}
\item{plants}{is a \link{data.frame} with the the same elements as \code{\link{plants.swo}}.}
\item{age}{is an integer value that represents the age of the plants,
in years.}
\item{x0}{is the $x_{0}$ coefficient for the Hann and Wang (1990) mortality model.}
\item{n.years.projected}{is the number of years that $x$ has been
	projected forward in time.}
}
}

\references{

Ritchie, M.W. 2008. User's Guide and Help System for CONIFERS: A Simulator for Young Conifer Plantations Version
4.10. See \url{http://www.fs.fed.us/psw/programs/ecology_of_western_forests/projects/conifers/}

}

\author{Jeff D. Hamann \email{jeff.hamann at forestinformatics.com},\cr
	     Martin W. Ritchie \email{mritchie at fs.fed.us} }

\seealso{    \code{\link{plants.smc}},
	     \code{\link{plots.smc}}
	     \code{\link{plants.swo}},
	     \code{\link{plots.swo}},
	     \code{\link{sample.data}},
	     \code{\link{set.species.map}},		
	     \code{\link{set.variant}},		
  	     \code{\link{smc}},
  	     \code{\link{summary.sample.data}},
	     \code{\link{swo}},
	     \code{\link{thin}}
}

\examples{
library( rconifers )
## Example for SWO variant
## set the variant to the SWO variant and set species map
##set.species.map( set.variant(0) )
set.variant(0)

## grow the data that was originally swo in the smc variant
# load and display CONIFERS example plots
data( plots.swo )
print( plots.swo )

# load and display CONIFERS example plants
data( plants.swo )
print( plants.swo )

# create the sample.data list object
sample.swo.3<- list( plots=plots.swo, plants=plants.swo, age=3, x0=0.0,n.years.projected=0)
class(sample.swo.3)<- "sample.data"


}

\keyword{models}

and the WARNING:

* checking Rd \usage sections ... WARNING
Assignments in \usage in documentation object 'sample.data':
   x<- list(plots, plants, age = 0, x0 = 0, n.years.projected = 0)
   class(x)<- "sample.data"

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd contents ... OK



Respectfully,
Jeff.


Jeff Hamann, PhD
PO Box 1421
Corvallis, Oregon 97339-1421
541-754-2457
jeff.hamann[at]forestinformatics[dot]com
jeff.d.hamann[at]gmail[dot]com
http://www.forestinformatics.com
http://en.wikipedia.org/wiki/Forest_informatics

To ensure that your email is processed, include a subject entry in your email.




On Jan 6, 2012, at 11:38 AM, Bryan Hanson wrote:

Jeff, quick question: is this a data set or a function you are documenting?  What you say sounds like it's data, but the Rd file reads more like a function.  Or are you trying to document a data format/object which stores specific data sets?

Let us know, and I'll bet the answer will appear pretty quickly. Bryan

***********
Bryan Hanson
Professor of Chemistry&  Biochemistry
DePauw University

On Jan 6, 2012, at 2:11 PM, Jeff Hamann wrote:

I'm trying to update a package and would like to crush a WARNING message for a clean build.

I've been struggling with this question and haven't gotten any traction on the web either.

I've got a document file (Rd) that contains the following \usage statement:

\name{sample.data}
\alias{sample.data}

\title{CONIFERS forest growth model sample data}

\description{ A list object of type \code{sample.data} stores all of
the basic information about a \code{\link{data.frame}} object
representing a sample of plants.}

\usage{
x<- list( plots=data.frame(), plants=data.frame(), age=0, x0=0.0, n.years.projected=0 )
class(x)<- "sample.data"
}

When I run R CMD check [pkg], I get the following WARNING:

* checking Rd \usage sections ... WARNING
Assignments in \usage in documentation object 'sample.data':
x<- list(plots, plants, age = 0, x0 = 0, n.years.projected = 0)
class(x)<- "sample.data"

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd contents ... OK

I'm not sure if there's a problem with the \alias section or the \usage section or both sections (I'm assuming this is the case).

I've read the Chapter 2 of R-ext.pdf plenty and just can't seem to see where I'm blowing it.

Respectfully,
Jeff.


Jeff Hamann, PhD
PO Box 1421
Corvallis, Oregon 97339-1421
541-754-2457
jeff.hamann[at]forestinformatics[dot]com
jeff.d.hamann[at]gmail[dot]com
http://www.forestinformatics.com
http://en.wikipedia.org/wiki/Forest_informatics

To ensure that your email is processed, include a subject entry in your email.





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