R devel - May 2007 - Imports/exports of S4 methods

I have a question about what to do in the following situation (please bear with 
the setup):

Package A defines an S4 generic 'foo' and as well as S4 methods for
'foo' and has

exportMethods("foo")

in its NAMESPACE file.

Package B defines another method for 'foo' for class "bar" and
has

importFrom(A, "foo")
exportMethods("foo")
exportClasses("bar")

in its NAMESPACE file.  Should Package B also have Package A in the
'Depends:'
field of the DESCRIPTION file or is it correct to import Package A only?

Finally, Package C has a single exported function named 'myfunc' which
needs to
use the method for 'foo' defined in Package B, so its NAMESPACE file has

importFrom(A, "foo")
importMethodsFrom(B, "foo")
importClassesFrom(B, "bar")
export("myfunc")

Is this the correct thing to do?

The error I get under this setup is that 'myfunc' cannot find the method
for
'foo' defined in Package B when 'myfunc' calls 'foo' on
an object of class "bar".

If you've made it this far I'm already grateful!  Any help with this
would be
appreciated.

-roger
-- 
Roger D. Peng  |  http://www.biostat.jhsph.edu/~rpeng/

I'm wrestling with the same issues, so this is the blind leading the 
blind,  but that usually prompts someone knowledgeable to say something 
useful.

Roger D. Peng wrote:
>I have a question about what to do in the following situation (please bear
with
>the setup):
>
>Package A defines an S4 generic 'foo' and as well as S4 methods for
'foo' and has
>
>exportMethods("foo")
>
>in its NAMESPACE file.
>
>Package B defines another method for 'foo' for class "bar"
and has
>
>importFrom(A, "foo")
>exportMethods("foo")
>exportClasses("bar")
>
>in its NAMESPACE file.  Should Package B also have Package A in the
'Depends:'
>field of the DESCRIPTION file or is it correct to import Package A only?
>  
>
I thought it should only be necessary to import A in NAMESPACE and list 
it in Imports in the DESCRPTION file,  but I get warning messages if the 
code in B does not require("A") in the .onLoad function.  This in turn
means that A needs to be in the Depends line of DESCRIPTION.
>Finally, Package C has a single exported function named 'myfunc'
which needs to
>use the method for 'foo' defined in Package B, so its NAMESPACE file
has
>
>importFrom(A, "foo")
>importMethodsFrom(B, "foo")
>importClassesFrom(B, "bar")
>export("myfunc")
>
>Is this the correct thing to do?
>  
>
I don't think you need the imports in this case, just the the export. 
You do need B (and thus implicitly A) in the Depends line of DESCRIPTION.
>The error I get under this setup is that 'myfunc' cannot find the
method for
>'foo' defined in Package B when 'myfunc' calls 'foo'
on an object of class "bar".
>  
>
I'm not sure why, but the one problem I have had is that when the syntax 
of the NAMESPACE file is messed up, you only get warnings when to 
require the package, but then you get errors when you try to use the 
functions.  Be sure to look back and see if you got warnings when you 
require("B").
>If you've made it this far I'm already grateful!  Any help with this
would be
>appreciated.
>  
>
Thanks, you just saved me writing up the same questions.
>-roger
>  
>
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