From jmc at r-project.org  Sun Mar 25 01:11:55 2012
From: jmc at r-project.org (John Chambers)
Date: Sat, 24 Mar 2012 17:11:55 -0700
Subject: [Rd] RC / methods package
In-Reply-To: <4F6E2EC7.2060001@gmail.com>
References: <4F6E2EC7.2060001@gmail.com>
Message-ID: <4F6E62CB.40109@r-project.org>



On 3/24/12 1:29 PM, Paul Gilbert wrote:
> (I think this is being caused by the new methods package in RC.)
Possibly, but the methods package isn't particularly "new" in its method 
selection.

We need to see the definition of the class.  The note implies that it 
inherits from both "MySQLConnection" and "dbObjectId", both of which 
have methods for coercing to "integer".  Hence the ambiguity.
>
> In the RC (March 24) some of my packages are generating a Note
>
> Note: Method with signature "MySQLConnection#integer" chosen for 
> function "coerce",
>  target signature "TSMySQLConnection#integer".
>  "dbObjectId#integer" would also be valid
>
> This is coming from a call to dbGetQuery() in package DBI. The method 
> with the signature "TSMySQLConnection#integer" is generated 
> automatically because TSMySQLConnection inherits from
> MySQLConnection. (More details below.)
>
> Is there a way to pass this information along to coerce when the 
> method is generated, or otherwise suppress the Note?
No.  Methods are inherited according to rules implied by the class 
inheritance; R doesn't allow you to override the inheritance, other than 
by being more explicit about the method definition.  (It's only a note, 
and IMO a relevant one.  Be glad the language isn't Dylan, which treats 
similar ambiguities as a programming error. :-))
>
> BTW,
>  1/ It would be nice if the Note mentioned what method is generating 
> it, in addition to the signature. Debugging for a call several levels 
> deep in the stack is already hard enough.
?? it does, for coerce()  which admittedly you have to know is the 
method defined for as(thing, "integer") either directly or indirectly.  
Unless you mean showing you the whole method definition, but that seems 
not relevant to selection.

If you wanted to see the coerce() method, you need to do 
showMethods("coerce"), but I don't think that's relevant.  As mentioned, 
it's the class hierarchy that matters.
>
>  2/ The note only seems to get generated on the first call and then 
> gets suppressed. This will be nice for users, but makes debugging 
> harder. Is there a way to prevent suppressing the message?
No.  the note is generated when an inherited method is found.  That 
method is then cached, so the computations required are (fortunately) 
not repeated.

It would be nice to have tools that the package writer could apply to 
generate all possible inheritance patterns, and flag possible 
ambiguities at package INSTALL time, as opposed to when the package is 
used.  But it's likely that would generate so many cases unlikely to 
occur that the package developer would ignore it, even assuming the 
developer was energetic enough to use the tool in the first place.
> o
>  3/ It seems strange that  getMethod() cannot find the methods even 
> though showMethods() shows it. (See below.)
I think you're confusing getMethod(), which only finds directly defined 
methods, with selectMethod() which replicates the inheritance computations.

In any case the selection of the method has been specified for you already.

John
>
> Paul
> ________
>
> >showMethods("dbGetQuery")
> Function: dbGetQuery (package DBI)
> conn="MySQLConnection", statement="character"
>
> >   z <- TSget("Series 1", con, TSrepresentation="timeSeries")
> Note: Method with signature "MySQLConnection#integer" chosen for 
> function "coerce",
>  target signature "TSMySQLConnection#integer".
>  "dbObjectId#integer" would also be valid
> Loading required package: zoo
>
> Attaching package: ?zoo?
>
> The following object(s) are masked from ?package:timeSeries?:
>
>     time<-
>
> The following object(s) are masked from ?package:base?:
>
>     as.Date, as.Date.numeric
>
> >  showMethods("dbGetQuery")
> Function: dbGetQuery (package DBI)
> conn="MySQLConnection", statement="character"
> conn="TSMySQLConnection", statement="character"
>     (inherited from: conn="MySQLConnection", statement="character")
>
> > getMethod("dbGetQuery",  signature = c("TSMySQLConnection", 
> statement="character"))
> Error in getMethod("dbGetQuery", signature = c("TSMySQLConnection", 
> statement = "character")) :
>   No method found for function "dbGetQuery" and signature 
> TSMySQLConnection, character
> >
>
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>



[Rd] RC / methods package
John Chambers