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NAMESPACE and bundle

6 messages · Paul Gilbert, Iago Mosqueira, Philippe GROSJEAN

Original
Iago Mosqueira
# 
Dear all,

I have a package that passes R CMD check, and shows no problems when using all its methods as declared in NAMESPACE. When this package is added to a bundle, which already consists of 5 packages, the examples in the Rd pages thta call a number of methods fail during the bundle check. These all passed when check is run on this package alone. Other packages in the bundle are very similar, in that all import all S4 classes and methods from the first package (using import("FLCore") in NAMESPACE) in the bundle, and export their own overloaded methods.

If I run check on a mini-bundle consisting only of the main package (FLCore) and this problematic package, it shows no problem. So I assume a problem of NAMESPACE conflict is the culprit, but experimnting with various package combinations, to try and isolate the conflict, has not worked. This package seems to conflict with every other secondary package.

I am dealing with internal dependencies by adding a require(FLCore) line to the .onLoad() call in zzz.R

Can anybody point me at what to look for? What could be the reason for this problem?

I hope the explanation was clear enough. Many thanks,


Iago


Dr. Iago Mosqueira

Marine Research Division
AZTI Tecnalia
Txatxarramendi Ugartea, z/g
48395 Sukarrieta - Bizkaia
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+34 946 029 448
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imosqueira at suk.azti.es
http://www.azti.es/
Paul Gilbert
# 
Iago

There is a problem that bundle checking works slightly differently than 
individual package checking in this regard.  I think it has to do with 
when the namespace gets registered, or something like that. As I recall, 
the work around is to explicitely require  the package in the test files 
for it. I.e. put
  require("pac")
in all the files in pac/tests.   If that does not work, let me know and 
I will look more carefully to find what I had to do.

Paul
Iago Mosqueira wrote:

            

      
      
      
    

        

      
      
    

        
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      Paul Gilbert
    

    

      
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Iago

I think your R code file  needs an .onLoad function.  Here is the 
..onLoad from my dse1 package which is in the dse bundle, as is tframe,  
along with comments which I had forgotten.

..onLoad  <- function(library, section) {
   .DSEflags(list(COMPILED=TRUE, DUP=TRUE))
   # next require is necessary for bundle check to run examples, 
   # but does not seem to be necessary when packages are not bundled
   require("tframe")
   invisible(TRUE)
   }


Hope this works,
Paul

        
Iago Mosqueira wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
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6 days later

    

      
      

        


  

        

      Iago Mosqueira
    

    

      
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El jue, 22-06-2006 a las 10:37 -0400, Paul Gilbert escribi?:

            

      
      
      
    

        
Hi,

Thanks for the tip. I already had an .onLoad() function, with 

.onLoad <- function(lib,pkg) {
	require(methods)
        require(FLCore)
}

the first to comply with the needs of an S4 package, the second to solve
the internal dependency that outside of the bundle is solved with
Depends: in DESCRIPTION.

Is there anything else I could look at?

Thanks,


Iago

        
Iago Mosqueira wrote:

        

            

      
      
      
    

        
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files,

            

      
      
      
    

        
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      Philippe GROSJEAN
    

    

      
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Iago Mosqueira wrote:

            

      
      
      
    

        
Hello Iago,

In principle, you should not use require() statements any more. 
Dependences should be resolved in the NAMESPACE and in Depends: field of 
description. It works for me for the SciViews bundle. I think that the 
situation is the same as for FLR: I have a svMisc package with basic 
functions, and all other packages depend on it, plus other complex 
interdependences between the other packages in the bundle.

You should really think twice before distributing a bundle: it is more 
of a problem. First, you force users to download and install the whole 
bundle (by definition!), even if they are interested by ony a part of 
it. Second, it is the same for updates: if you change something in one 
package, you must upload the whole bundle.

Now that dependencies are nicely resolved during R package installation, 
  bundles are not so attracting, and I would advise to continue 
distributing your packages separately.

Best,

Philippe Grosjean