From geoff.lee99 at gmail.com  Thu Mar 12 21:47:21 2015
From: geoff.lee99 at gmail.com (Geoff Lee)
Date: Fri, 13 Mar 2015 07:47:21 +1100
Subject: [Rd] Understanding why "no metadata object found ... not exported?"
	warnings from the methods package exist, and what they mean
Message-ID: <00b601d05d05$c0a73e70$41f5bb50$@gmail.com>

Hi

 

I am seeking to understand why the methods package (to be specific
`methods:::.findOrCopyClass` when called by `setIs` when called by
`setClass`) emits a warning message such as

 

` class "SpatialLinesNULL" is defined (with package slot 'rgeos') but no
metadata object found to revise subclass information---not exported?  Making
a copy in package 'minweSpatialNULL `

 

when I try to `R cmd build .` and then R cmd check *.gz` (or alternatively
`devtools::load_all()`) the package I am building.

 

What I don't really follow is why I am being warned when evidently the
methods package *can* actually find the metadata object in order to make a
copy of it (or does it just copy a name which binds to the original metadata
object - I'm not clear on that).  What is the danger I am being warned
about, and what, ideally should I do about it?  

 

In practice I know I can make the message go away by using
`importClassesFrom(rgeos,SpatialLinesNULL)` in my NAMESPACE file now that
Edzer Pebesma has arranged for a version of rgeos which exports
SpatialLinesNULL.  

 

But why do I need to explicitly import the superclass of the class I am
actually using?  If I were using a *function* from rgeos, which in turn
utilised a second non-exported function from rgeos, the package namespace
environments mechanism would take care of how to find and access that second
function, silently.  It wouldn't warn me about it and make me import it - in
fact avoiding that is as I understand it a major purpose of the packaging
namespace process.

 

There is obviously something I am missing, but having thought and read for
several days I am at a loss as to what.

 

Thanks heaps in advance for any illumination that you can offer me!

 

What I have done already.

 

I have a toy example in folder SpatialLinesNULL of branch SpatialLinesNULL
in a github repo at http://github.com/Geoff99/Examples/tree/SpatialLinesNULL

 

I have asked a (far too) long question on Stack Overflow (see
http://stackoverflow.com/questions/28871632/how-to-resolve-warning-messages-
metadata-object-not-found-spatiallinesnull-cla/29010169#29010169), the
specific aspect of which was very kindly and quickly answered by Edzer
Pebesma.

 

I have read the methods documentation ( which was very valuable indeed) and
have posted my understanding of what I learnt from that (and from stepping
through my toy example in the debugger) as a (once again quite long) answer
on Stack Overflow here

 

http://stackoverflow.com/questions/28871632/how-to-resolve-warning-messages-
metadata-object-not-found-spatiallinesnull-cla/29010169#29010169

 

PS If I should be asking this somewhere else, please just say.

 

PPS The primary purpose of the package I am building (not the toy example)
is to help me learn about programming and packaging in R, hence my desire to
chase down and understand this warning fully.


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[Rd] Understanding why "no metadata object found ... not exported?" warnings from the methods package exist, and what they mean
Geoff Lee