Ok, I could solve also the latter problem by defining show.myclass function
in the zzz.R file and adding the line 'S3method(show,myclass)' into
NAMESPACE file. Now the package passes all checks.
The information on how to exactly extend existing methods and include new
methods/classes into a package is available but rather scattered in the web.
A step-by-step tutorial written by an experienced user who is aware of best
practices etc. would be rather useful for a beginner.
best regards
Leo
On Mon, Jul 20, 2009 at 7:09 PM, L L <lmla...@gmail.com> wrote:
> Thanks, the issue was solved by adding class definitions to the zzz.R file
> in the R code directory. However, this led to a new problem.
>
> The zzz.R now contains class definition:
>
> > setClass("myclass", contains = "list")
>
> and method definition for the new class, extending the generic 'show':
>
> > setGeneric("show",function(x,...){standardGeneric("show")})
> > setMethod("show", "myclass",function(x, ...) {cat("myclass object \n")})
>
> I get two warnings. The first one:
>
> * checking Rd files ... WARNING
> Rd files with duplicated alias 'show,myclass-method':
> myclass-class.Rd show-methods.Rd
>
> I get this one because the alias row for the method
> (\alias{show,myclass-method}) is in both myclass-class.Rd file and
> show-methods.Rd file (created by promptMethods function). This is likely
> related to the second warning:
>
> * checking for missing documentation entries ... WARNING
> Undocumented code objects:
> show
>
> I thought that the show method would've been documented correctly as I put
> 'show-methods.Rd' file in the 'man' directory. This does not seem to be the
> case, however.
>
> Any help on how I should document the extended show method in this case, or
> are there some mistakes in my original definition for extended 'show'? I
> could not find suitable examples from the web/mailing lists.
>
> br
> Leo
>
>
>
> On Fri, Jul 10, 2009 at 5:37 AM, Martin Morgan <mtmor...@fhcrc.org> wrote:
>
>> L L wrote:
>> > Dear all,
>> >
>> > I have been trying to create an R package. This has been successfull
>> until I
>> > tried to define classes.
>> >
>> > Currently, my procedure is the following:
>> >
>> > Start R, load the function and class definition
>> >> tmp <- function (x) {x}
>> >> setClass("rpa", contains = "list", where=topenv(parent.frame()))
>> >
>> > Use package skeleton to create directory structure:
>> >> package.skeleton(name = "test",list=c("tmp"))
>>
>> I don't think package.skeleton knows to copy the class definition to the
>> R files; I think you have to do that yourself -- is there a
>> setClass("rpa", contains="list") instruction in the R files created by
>> package.skeleton?
>>
>> Martin
>> >
>> > Edit man files, add test/NAMESPACE file with the following contents:
>> >> export(tmp)
>> >> exportClasses("rpa")
>> >
>> > Use R CMD check and R CMD build to create tarball.
>> > -> No error messages.
>> >
>> > Start R, install the created package:
>> >> install.packages("test_1.0.tar.gz",repos=NULL)
>> >
>> > Test the new package:
>> >> require(test)
>> >> my.object = new("rpa")
>> >
>> > This gives the error message
>> >> Error in getClass(Class, where = topenv(parent.frame())) :
>> >> "rpa" is not a defined class
>> >
>> > Any tips on how to define and export global classes in package creation?
>> >
>> > I also tried
>> > - to replace the 'topenv(parent.frame())' with '.GlobalEnv' in setClass.
>> > - place the setClass within function 'tmp'
>> > - exportClasses(rpa) in the namespace (without suffixes "")
>> >
>> > I paged through the related mailing list discussions but could not find
>> a
>> > solution. Any tips and tricks would be worthwhile now; I guess this
>> should
>> > be a standard issue but it seems a bit tricky to come up with a quick
>> > solution with the little programming experience that I have.
>> >
>> > kind regards
>> > Leo Lahti
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-help@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
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