R devel - Aug 2013 - Correct NAMESPACE approach when writing an S3 method for a generic in another package

Dear List,

In one of my packages I have an S3 method for the plot3d generic
function from package rgl. I am trying to streamline my Depends
entries but don't know how to have

plot3d(foo)

in the examples section for the plot3d method in my package, without
rgl being in Depends.

Note that I importFrom(rgl, plotd3d) and register my S3 method via
S3Method() in the NAMESPACE.

If rgl is not in Depends but in Imports, I see this when checking the package
> ## 3D plot of data with curve superimposed
> plot3d(aber.pc, abernethy2)
Error: could not find function "plot3d"

I presume this is because rgl's namespace is only loaded but the
package is not attached to the search path.

Writing R extensions indicates that one can export from a namespace
something that was imported from another package namespace. I thought
that might help the situation, and now the code doesn't raise an
error, I get

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ?plot3d?
All user-level objects in a package should have documentation entries.
See the chapter ?Writing R documentation files? in the ?Writing R
Extensions? manual.

as I don't document plot3d() itself.

What is the recommended combination of Depends and Imports plus
NAMESPACE directives etc that one should use in this situation? Or am
I missing something else?

I have a similar issue with my package including an S3 method for a
generic in the lattice package, so if possible I could get rid of both
of these from Depends if I can solve the above issue.

Thanks in advance.

Gavin

-- 
Gavin Simpson

What I do, which is probably wrong, but at least it works, is export
the s3 method as a function. i.e. instead of

S3method(genericfunction, myclass)

I do

export(genericfunction.myclass)

Hadley

On Fri, Aug 23, 2013 at 11:01 PM, Gavin Simpson <ucfagls at gmail.com>
wrote:
> Dear List,
>
> In one of my packages I have an S3 method for the plot3d generic
> function from package rgl. I am trying to streamline my Depends
> entries but don't know how to have
>
> plot3d(foo)
>
> in the examples section for the plot3d method in my package, without
> rgl being in Depends.
>
> Note that I importFrom(rgl, plotd3d) and register my S3 method via
> S3Method() in the NAMESPACE.
>
> If rgl is not in Depends but in Imports, I see this when checking the
package
>
>> ## 3D plot of data with curve superimposed
>> plot3d(aber.pc, abernethy2)
> Error: could not find function "plot3d"
>
> I presume this is because rgl's namespace is only loaded but the
> package is not attached to the search path.
>
> Writing R extensions indicates that one can export from a namespace
> something that was imported from another package namespace. I thought
> that might help the situation, and now the code doesn't raise an
> error, I get
>
> * checking for missing documentation entries ... WARNING
> Undocumented code objects:
>   ?plot3d?
> All user-level objects in a package should have documentation entries.
> See the chapter ?Writing R documentation files? in the ?Writing R
> Extensions? manual.
>
> as I don't document plot3d() itself.
>
> What is the recommended combination of Depends and Imports plus
> NAMESPACE directives etc that one should use in this situation? Or am
> I missing something else?
>
> I have a similar issue with my package including an S3 method for a
> generic in the lattice package, so if possible I could get rid of both
> of these from Depends if I can solve the above issue.
>
> Thanks in advance.
>
> Gavin
>
> --
> Gavin Simpson
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


-- 
Chief Scientist, RStudio
http://had.co.nz/

I think rgl should be in Depends.  You are providing a method for a
generic function from another package. In order to use your method, you
want the user to be able to call the generic function without scoping
(i.e. without calling rgl::plot3d), so the generic should be on the
search path, so the package that provides it should be listed in Depends
in the NAMESPACE file.

Martyn

On Fri, 2013-08-23 at 22:01 -0600, Gavin Simpson wrote:
> Dear List,
> 
> In one of my packages I have an S3 method for the plot3d generic
> function from package rgl. I am trying to streamline my Depends
> entries but don't know how to have
> 
> plot3d(foo)
> 
> in the examples section for the plot3d method in my package, without
> rgl being in Depends.
> 
> Note that I importFrom(rgl, plotd3d) and register my S3 method via
> S3Method() in the NAMESPACE.
> 
> If rgl is not in Depends but in Imports, I see this when checking the
package
> 
> > ## 3D plot of data with curve superimposed
> > plot3d(aber.pc, abernethy2)
> Error: could not find function "plot3d"
> 
> I presume this is because rgl's namespace is only loaded but the
> package is not attached to the search path.
> 
> Writing R extensions indicates that one can export from a namespace
> something that was imported from another package namespace. I thought
> that might help the situation, and now the code doesn't raise an
> error, I get
> 
> * checking for missing documentation entries ... WARNING
> Undocumented code objects:
>   ?plot3d?
> All user-level objects in a package should have documentation entries.
> See the chapter ?Writing R documentation files? in the ?Writing R
> Extensions? manual.
> 
> as I don't document plot3d() itself.
> 
> What is the recommended combination of Depends and Imports plus
> NAMESPACE directives etc that one should use in this situation? Or am
> I missing something else?
> 
> I have a similar issue with my package including an S3 method for a
> generic in the lattice package, so if possible I could get rid of both
> of these from Depends if I can solve the above issue.
> 
> Thanks in advance.
> 
> Gavin
>