From D.Strbenac at garvan.org.au  Wed Apr 20 06:15:09 2011
From: D.Strbenac at garvan.org.au (Dario Strbenac)
Date: Wed, 20 Apr 2011 14:15:09 +1000 (EST)
Subject: [Rd] Package Name Not Found Warning
Message-ID: <20110420141509.BLN46734@gimr.garvan.unsw.edu.au>

Ah yes, I found it now. I had the exact same setOldClass statement at the top of 2 different R files. Having it in the first collated one solves my problem.

---- Original message ----
>Date: Tue, 19 Apr 2011 20:29:40 -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 08:00 PM, Dario Strbenac wrote:
>> Ah, I think it's happening because I have
>>
>> setOldClass(AffymetrixCelSet) in my package.
>
>if AffymetrixCelSet is from aroma.affymetrix, then the line above results in
>
> > setOldClass(AffymetrixCelSet)
>Error in x[length(x):1L] : object of type 'closure' is not subsettable
>
>maybe you meant
>
>setOldClass("AffymetrixCelSet")
>
>but if I put that in a package that either Depends: or not on 
>aroma.affymetrix then I don't see the warning in your original report. 
>I'm not sure you've diagnosed the problem correctly?
>
>Martin
>
>>
>> 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
>
>
>-- 
>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