RC / methods package
On 12-03-25 05:29 PM, Paul Gilbert wrote:
John
Here is the definition of the TSMySQLConnection class, and a few other
things. This is a simplified example that produces the message, but
unfortunately will not work unless you have a MySQL database to connect
to. (I do get the same problem with PostgreSQL, and may with SQLLite,
but I have not tested the last yet.)
require("methods")
require("DBI")
require("RMySQL")
setClassUnion("OptionalPOSIXct", c("POSIXct", "logical"))
setClass("conType", representation( drv="character"), "VIRTUAL" )
setClass("TSdb", representation( dbname="character",
hasVintages="logical", hasPanels="logical"), "VIRTUAL" )
setClass("TSMySQLConnection", contains=c("MySQLConnection", "conType",
"TSdb"))
setGeneric("TSconnect", def= function(drv, dbname, ...)
standardGeneric("TSconnect"))
setMethod("TSconnect", signature(drv="MySQLDriver", dbname="character"),
definition=function(drv, dbname, ...) {
con <- dbConnect(drv, dbname=dbname, ...)
new("TSMySQLConnection" , con, drv="MySQL", dbname=dbname,
hasVintages=dbExistsTable(con, "vintageAlias"),
hasPanels =dbExistsTable(con, "panels"))
})
con <- TSconnect(dbDriver("MySQL"), "test")
dbGetQuery(con, "show tables")
Note: Method with signature "MySQLConnection#integer" chosen for
function "coerce",
target signature "TSMySQLConnection#integer".
"dbObjectId#integer" would also be valid
Tables_in_test
1 A
2 B
>
The message also seems to go away, even quitting R and restarting to
clear the cache, if I change the TSconnect method as follow
setMethod("TSconnect", signature(drv="MySQLDriver", dbname="character"),
definition=function(drv, dbname, ...) {
con <- dbConnect(drv, dbname=dbname, ...)
new("TSMySQLConnection" , con, drv="MySQL", dbname=dbname,
hasVintages=FALSE,
hasPanels =FALSE)
})
Why this would happen makes absolutely no sense to me. In the first
version is dbExistsTable(con, "vintageAlias") left unevaluated in the
result from new?
This is very strange. With
setMethod("TSconnect", signature(drv="MySQLDriver", dbname="character"),
definition=function(drv, dbname, ...) {
con <- dbConnect(drv, dbname=dbname, ...)
hasVintages <- as.logical(dbExistsTable(con, "vintageAlias") )
hasPanels <- as.logical(dbExistsTable(con, "panels") )
new("TSMySQLConnection" , con, drv="MySQL", dbname=dbname,
hasVintages=FALSE,
hasPanels =FALSE)
})
I get the note, but if I remove the two lines that appear to do nothing:
setMethod("TSconnect", signature(drv="MySQLDriver", dbname="character"),
definition=function(drv, dbname, ...) {
con <- dbConnect(drv, dbname=dbname, ...)
new("TSMySQLConnection" , con, drv="MySQL", dbname=dbname,
hasVintages=FALSE,
hasPanels =FALSE)
})
I no longer get the note. I am restarting R each time to be sure nothing
is cached.
[ R version 2.15.0 RC (2012-03-25 r58832) ]
Paul
As you can tell, I'm struggling a bit with interpreting the information from the note. Also, if it were a warning I could set it to stop, and then traceback to what was causing the problem. As it is, it took me a fairly long time just to get the fact that the call to dbGetQuery() was generating the message. And caching the methods may be good for performance, but when things change the second time you call them it sure makes debugging difficult. Best, Paul On 12-03-25 03:24 PM, John Chambers wrote:
On 3/24/12 5:43 PM, Paul Gilbert wrote:
On 12-03-24 08:11 PM, John Chambers wrote:
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.
Is there a way to know which class it is that we need to see the definition for?
It's in the note: 'target signature "TSMySQLConnection#integer"'. In functional OOP with multiple dispatch, it's all the classes that matter in general, but in this and most cases, one class is likely the relevant one: "TSMySQLConnection". That was why I said what I did before. (We could go to a bit more effort and back-translate the dispatch string "TSMySQLConnection#integer" into the corresponding formal arguments. Would be more natural with the INSTALL time tool I mentioned before. That's the real challenge here -- to give information about this to the package developer, not the poor user.) John
Paul
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
______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel