From D.Strbenac at garvan.org.au  Wed Apr 20 05:00:38 2011
From: D.Strbenac at garvan.org.au (Dario Strbenac)
Date: Wed, 20 Apr 2011 13:00:38 +1000 (EST)
Subject: [Rd] Package Name Not Found Warning
In-Reply-To: <4DAE4398.4060805@fhcrc.org>
References: <20110420100014.BLN40994@gimr.garvan.unsw.edu.au>
	<4DAE4398.4060805@fhcrc.org>
Message-ID: <20110420130038.BLN45351@gimr.garvan.unsw.edu.au>

Ah, I think it's happening because I have 

setOldClass(AffymetrixCelSet) in my package.

I guess I need to use there where argument. But how do I have this call outside any S4 functions, but without having to load aroma.affymetrix when my package loads ?

---- Original message ----
>Date: Tue, 19 Apr 2011 19:23:20 -0700
>From: Martin Morgan <mtmorgan at fhcrc.org>  
>Subject: Re: [Rd] Package Name Not Found Warning  
>To: D.Strbenac at garvan.org.au
>Cc: r-devel at r-project.org
>
>On 04/19/2011 05:00 PM, Dario Strbenac wrote:
>> Hello,
>>
>> I've got a DESCRIPTION file with a the first line:
>>
>> Package: Repitools
>>
>> But, when I run R CMD INSTALL Repitools I get:
>>
>> * installing *source* package Repitools ...
>> ** R
>> ** data
>> ** inst
>> ** preparing package for lazy loading
>> Warning in FUN(X[[1L]], ...) :
>>    Created a package name, "2011-04-20 09:05:40", when none found
>
>For what it's worth, this comes up when a class is being created in an 
>environment that is not the global environment or does not have a 
>variable .packageName, apparently added early in the name space creation 
>process. You can mimic this with
>
>   setClass("A", where=new.env())
>
>or
>
>   local({ setClass("A", where=environment()) })
>
>Kind of doubt whether you've actually done something like that in your 
>package, but maybe it twigs something...
>
>Also, if you add
>
>   trace(methods::getPacakgeName, quote(print(where)))
>
>or
>
>   trace(warning, quote(print(sys.calls())))
>
>somewhere early in your package (the top of the first file to be 
>collated) you'll get messages that might point to where things are going 
>wrong.
>
>Hope that helps,
>
>Martin
>
>> ** help
>> *** installing help indices
>> ** building package indices ...
>> ** testing if installed package can be loaded
>>
>> * DONE (Repitools)
>>
>> It looks like it knows about the package name at the start and end of the process, but not in the middle of it.
>>
>> Loading the packing in an R session and looking at the sessionInfo shows the package name was properly processed. Is this a spurious warning ?
>>
>> I'm using:
>> R version 2.13.0 (2011-04-13)
>> Platform: x86_64-unknown-linux-gnu (64-bit) (actually Ubuntu 10.10)
>>
>> --------------------------------------
>> Dario Strbenac
>> Research Assistant
>> Cancer Epigenetics
>> Garvan Institute of Medical Research
>> Darlinghurst NSW 2010
>> Australia
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>-- 
>Computational Biology
>Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
>Location: M1-B861
>Telephone: 206 667-2793


--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia



[Rd] Package Name Not Found Warning
Dario Strbenac