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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