From pgilbert at bank-banque-canada.ca  Mon May  5 03:46:18 2008
From: pgilbert at bank-banque-canada.ca (Paul Gilbert)
Date: Sun, 04 May 2008 21:46:18 -0400
Subject: [Rd] S4 / S3 / Sweave problem
In-Reply-To: <alpine.LFD.1.10.0805041736420.2977@auk.stats.ox.ac.uk>
References: <481DDF0E.6060509@bank-banque-canada.ca>
	<alpine.LFD.1.10.0805041736420.2977@auk.stats.ox.ac.uk>
Message-ID: <481E66EA.5010408@bank-banque-canada.ca>



Prof Brian Ripley wrote:
> I'm not sure what the issue being asked about here is.  The peculiar 
> printing I don't see and may well be a locale issue.  (Is this UTF-8 and 
> TeX has not been told so?)

It seems to happen in locales UTF-8, POSIX and C.  I have not tried others.

> 
> The other issue is that when printing an object with attributes, there 
> is no consideration of S4 classes amongst the attributes.  That was 
> either an undocumented design decision or an omission.  This is 
> different from
> 
>> print(attributes(zz))
> $tsp
> [1]  1 10  1
> 
> $class
> [1] "ts"
> 
> $Meta
> An object of class ?TSmetax?
> Slot "serIDs":
> [1] "whatever"
> 
> Slot "ExtractionDate":
> NULL
> 
> since although attributes are internally a pairlist and printed by a 
> special C function, attributes() returns a list.
> 
> It would be fairly easy to include a branch for S4 objects, but there 
> are ambuiguities still over what they are (I wrote up a set of questions 
> over a year ago about this).  But it would seem fairly safe to send them 
> to show() in the same circumstances that autoprinting does for 
> apparently S4 objects.

Yes, I do have the impression that print() does not do exactly what one 
might like when it finds an S4 attribute in an S3 object. I hope this is 
not a design decision. It would make it very difficult to migrate toward 
S4 if it is not possible to include S4 objects in S3 objects this way.
> 
> On Sun, 4 May 2008, Paul Gilbert wrote:
> 
>> I'm not sure if this as a bug or something I am doing wrong. It occurs 
>> in both 2.7.0 and 2.6.2.
> 
> My guess is that it was never intended that S4 objects be used as
> attributes, in the same way that one of the unanswered questions is if S4
> objects should be allowed to have attributes (other than slots).
> 
>>
>> require("methods")
>>
>> setClassUnion("OptionalPOSIXct",   c("POSIXct",   "NULL"))
>>
>> setClass("TSmetax",
>>  representation(serIDs="character", ExtractionDate="OptionalPOSIXct" ))
>>
>> setGeneric("TSmetax",
>>   def= function(x, ...) standardGeneric("TSmetax"))
>>
>> setMethod("TSmetax",   signature(x="character"),
>>   definition= function(x, ...){
>>       new("TSmetax", serIDs=x, ExtractionDate=Sys.time())
>>       } )
>>
>>> z <- new("TSmetax", serIDs="whatever", ExtractionDate= NULL)
>>> print(z)
>> An object of class "TSmetax"
>> Slot "serIDs":
>> [1] "whatever"
>>
>> Slot "ExtractionDate":
>> NULL
>>
>> Now if I make this an attribute of an S3 class an print, I get
>>> zz <- ts(1:10)
>>> attr(zz, "Meta") <- z
>>> print(zz)
>> Time Series:
>> Start = 1
>> End = 10
>> Frequency = 1
>> [1]  1  2  3  4  5  6  7  8  9 10
>> attr(,"Meta")
>> <S4 Type Object>
>> attr(,"serIDs")
>> [1] "whatever"
>> attr(,"ExtractionDate")
>> `NULL`
>> attr(,"class")
>> [1] "TSmetax"
>> attr(,"class")attr(,"package")
>> [1] ".GlobalEnv"
>>>
>>
>> The `NULL` shows up i
>> shows up in the tex file generated by a vignette as
>> <soh>NULL<soh> which causes  tex (pdftex) to throw an  error.
>> (It also seems to mess up my mail tool, so I hope this goes through.)
> 
> 
====================================================================================

La version fran?aise suit le texte anglais.

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[Rd] S4 / S3 / Sweave problem
Paul Gilbert