On 12-03-26 02:47 PM, John Chambers wrote:
This direction is perhaps adding to the confusion rather than reducing it.
Let's go back to the original note:
Note: Method with signature "MySQLConnection#integer" chosen for
function "coerce",
target signature "TSMySQLConnection#integer".
"dbObjectId#integer" would also be valid
The purpose of the note is just to make you (the programmer) aware that
in fact two methods are available for coercing from "TSMySQLConnection"
to "integer". Which do you want, if either?
If it's not the one from "MySQLConnection" then one needs to say
explicitly what it should be. In any case, being explicit would remove
the note, if that's what is bothering people.
The "coerce" generic is abnormal, in that its methods are rarely
specified directly, but via a setAs() call and it's never invoked
directly, but rather from an as(thing, "integer")--this may in part be
why the behavior is confusing.
If you have an example that produces the note, the relevant methods can
be examined by following that example with
getMethod("coerce", c("MySQLConnection","integer"))
getMethod("coerce", c("dbObject","integer"))
You DO have to wait until the note is produced because the as()
calculations may install methods for coerce() in response to particular
calls.
Then it's likely you want to insert a
setAs("TSMySQLConnection", "integer", ....)
into the package that defines "TSMySQLConnection", with the chosen
definition.
Ok, if I understand correctly, when my code made the call to
dbExistsTable(), a method for "coerce" with signature
c("MySQLConnection","integer") was automatically generated. I can see
that when I do showMethods("coerce"):
from="MySQLConnection", to="integer"
(inherited from: from="dbObjectId", to="integer")
and also from looking at the RMySQL package source and seeing that
setAs("MySQLConnection", "integer", ....)
has not been done.
Then when I execute
dbGetQuery(con, "show tables")
the note reflects that it has to choose between the automatically
generated one and the one that the automatically generated one was
inherited from, so there is an ambiguity. If I do not do dbExistsTable()
first, then the automatically generated one has not been generated yet,
so there is no ambiguity and I do not get the note.
I can prevent getting the note by using
setAs("TSMySQLConnection", "integer",
def=getMethod("coerce", c("dbObjectId","integer")))
in my package. It make sense to specify the original rather than the
automatically generated one, but I am still a bit confused why the note
says it is using the automatically generated one, but if I try to set
that one explicitly I get an error:
> 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
> setAs("TSMySQLConnection", "integer",
+ def=getMethod("coerce", c("MySQLConnection","integer")))
Error in getMethod("coerce", c("MySQLConnection", "integer")) :
No method found for function "coerce" and signature MySQLConnection,
integer
>
(A this point I think I have a fix, so this is just for my general
understanding.)
Just to repeat: This is a "Note" and doesn't necessarily indicate a bug.
Even though in my case either would have worked, my feeling is that
there could be cases where it is a problem, so package developers should
be using setAs() explicitly to reduce ambiguities, as you say. And
because of this you should be issuing a warning not just a note. And, if
you do issue a warning, then that makes it a bug in my package, so I
want to fix it.
Thanks again,
Paul
It's in the nature of functional OOP with multiple dispatch that there
can be multiple eligible methods. It may or may not matter which is
chosen, and one can't guarantee that any automatic selection will get
the "right" one. It's nearly always helpful to be as specific as
possible where ambiguities do exist.
John
On 3/26/12 6:23 AM, Paul Gilbert wrote:
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
>
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