From ripley at stats.ox.ac.uk  Tue Sep 25 10:18:09 2007
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue, 25 Sep 2007 09:18:09 +0100 (BST)
Subject: [Rd] 'load' does not properly add 'show' methods for classes
 extending 'list'
In-Reply-To: <6phbqbrzjc3.fsf@gopher4.fhcrc.org>
References: <6phbqbrzjc3.fsf@gopher4.fhcrc.org>
Message-ID: <Pine.LNX.4.64.0709250751330.19522@gannet.stats.ox.ac.uk>

I am not sure why you expected this to work: I did not expect it to and 
could not find relevant documentation to suggest it should.

Loading an object created from a non-attached package does not in general 
attach that package and make the methods for the class of 'x' available. 
We have talked about attaching the package defining the class when an S4 
object is loaded, and that is probably possible now S4 objects can be 
unambiguously distinguished (although I still worry about multiple 
packages with the same generic and their order on the search path).

In your example there is no specific 'show' method on the search path when 
'show' is called via autoprinting in the second session, so 'showDefault' 
is called.  Package GSEABase gets attached as an (undocumented) side 
effect of calling 'getClassDef' from 'showDefault'.  I can see no 
documentation (and in particular not in ?showDefault) that 'showDefault' 
is supposed to attach the package defining the class and re-dispatch to a 
'show' method that package contains.  Since attaching packages behind the 
user's back can have nasty side effects (the order of the search path does 
mattter), I think the pros and cons need careful consideration: a warning 
along the lines of

   'object 'x' is of class "GeneSetCollection" from package 'GSEABase'
   which is not on the search path

might be more appropriate.  Things would potentially be a lot smoother if 
namespaces could be assumed, as loading a namespace has few side effects 
(and if loading a namespace registered methods for visible S4 generics 
smoothly).

Until I see documentation otherwise, I will continue to assume that I do 
need to attach the class-defining package(s) for things to work correctly.


On Mon, 24 Sep 2007, Martin Morgan wrote:

> The GeneSetCollection class in the Bioconductor package GSEABase
> extends 'list'
>
>> library(GSEABase)
>> showClass("GeneSetCollection")
>
> Slots:
>
> Name:  .Data
> Class:  list
>
> Extends:
> Class "list", from data part
> Class "vector", by class "list", distance 2
> Class "AssayData", by class "list", distance 2
>
> If I create an instance of this class and serialize it
>
>> x <- GeneSetCollection(GeneSet("X"))
>> x
> GeneSetCollection
>  names: NA (1 total)
>> save(x, file="/tmp/x.rda")
>
> and then start a new R session and load the data object (without first
> library(GSEABase)), the 'show' method is not added to the appropriate
> method table.
>
>> load("/tmp/x.Rda")
>> x
> Loading required package: GSEABase
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: AnnotationDbi
> Loading required package: DBI
> Loading required package: RSQLite
> An object of class "GeneSetCollection"
> [[1]]
> setName: NA
> geneIds: X (total: 1)
> geneIdType: Null
> collectionType: Null
> details: use 'details(object)'
>
> Actually, the behavior is more complicate than appears; in a new R
> session after loading /tmp/x.Rda, if I immediately do x[[1]] I get the
> show,GeneSetCollection-method but not show,GeneSet-method.
>
> Sorry for the somewhat obscure example.
>
> Martin
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] 'load' does not properly add 'show' methods for classes extending 'list'
Prof Brian Ripley