R devel - Jul 2007 - S4 coerce

(I am not sure if this is a bug or a request for a more understandable 
warning, or possible something obvious I should be posting on r-help.)

I am trying to coerce an new class object to be a DBIConnection and it 
does not work the way I think it should:

R version 2.5.1 (2007-06-27) ...
 > require("RMySQL") # or require("RSQLite")
Loading required package: RMySQL
Loading required package: DBI
[1] TRUE
 > m <- dbDriver("MySQL")  # or  m <-
dbDriver("SQLite")
 > con <- dbConnect(m, dbname="test")
 > dbGetQuery(con, "create table zzz (
+    vintage     VARCHAR(20) NOT NULL,
+    alias       VARCHAR(20) default NULL,
+    Documentation     TEXT,
+    PRIMARY KEY (vintage)
+    );")
NULL
 > dbListTables(con)
  [1] "zzz"
 > setClass("TSconnection",
representation(con="DBIConnection",
+    vintage = "logical",
+    panel   = "logical")
+    )
[1] "TSconnection"
 > setAs("TSconnection", "DBIConnection", def =
function(from) from at con)
 > setIs("TSconnection", "DBIConnection", coerce =
function(x) x at con)
Warning messages:
1: there is no automatic definition for as(object, "DBIConnection")
<-
value when object has class "TSconnection" and no 'replace'
argument was
supplied; replacement will be an error in: makeExtends(class1, class2, 
coerce, test, replace, by, classDef1 = classDef,
2: methods currently exist for coercing from "TSconnection" to 
"DBIConnection"; they will be replaced. in: 
..removePreviousCoerce(class1, class2, where, prevIs)

# (warning may be important, but I don't understand it)

 > setAs("TSconnection", "MySQLConnection", def =
function(from) from at con)
 > setIs("TSconnection", "MySQLConnection", coerce =
function(x) x at con)
Warning messages:
1: there is no automatic definition for as(object, "MySQLConnection")
<-
value when object has class "TSconnection" and no 'replace'
argument was
supplied; replacement will be an error in: makeExtends(class1, class2, 
coerce, test, replace, by, classDef1 = classDef,
2: methods currently exist for coercing from "TSconnection" to 
"MySQLConnection"; they will be replaced. in: 
..removePreviousCoerce(class1, class2, where, prevIs)

 > # or
 > # setAs("TSconnection", "SQLiteConnection", def =
function(from)
from at con)
 > # setIs("TSconnection", "SQLiteConnection", coerce =
function(x) x at con)

 > Tcon <- new("TSconnection", con=dbConnect(m,
dbname="test"),
vintage=FALSE, panel=FALSE)
 > is(Tcon, "DBIConnection")
[1] TRUE
 > is(Tcon, "MySQLConnection")
[1] TRUE
 > # or is(Tcon, "SQLiteConnection")

 > # This fails but I think it should work
 > dbListTables(Tcon)
Error in slot(from, "Id") : no slot of name "Id" for this
object of
class "TSconnection"

#these all work
 > dbListTables(Tcon at con)
  [1] "zzz"
 > dbListTables(as(Tcon, "MySQLConnection") )
  [1] "zzz"
 > dbListTables(as(Tcon, "DBIConnection") )
  [1] "zzz"
 >

Is this a bug or am I doing something wrong?

Thanks,
Paul Gilbert
===================================================================================
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Paul Gilbert <pgilbert at bank-banque-canada.ca> writes:
> (I am not sure if this is a bug or a request for a more understandable 
> warning, or possible something obvious I should be posting on r-help.)
>
> I am trying to coerce an new class object to be a DBIConnection and it 
> does not work the way I think it should:
>
> R version 2.5.1 (2007-06-27) ...
>  > require("RMySQL") # or require("RSQLite")
> Loading required package: RMySQL
> Loading required package: DBI
> [1] TRUE
>  > m <- dbDriver("MySQL")  # or  m <-
dbDriver("SQLite")
>  > con <- dbConnect(m, dbname="test")
>  > dbGetQuery(con, "create table zzz (
> +    vintage     VARCHAR(20) NOT NULL,
> +    alias       VARCHAR(20) default NULL,
> +    Documentation     TEXT,
> +    PRIMARY KEY (vintage)
> +    );")
> NULL
>  > dbListTables(con)
>   [1] "zzz"
>  > setClass("TSconnection",
representation(con="DBIConnection",
> +    vintage = "logical",
> +    panel   = "logical")
> +    )
> [1] "TSconnection"
>  > setAs("TSconnection", "DBIConnection", def =
function(from) from at con)
I think things work as you expect up until this pint.
>  > setIs("TSconnection", "DBIConnection", coerce =
function(x)
>  > x at con)
I'm confused about what you want to do here.  If you want TSconnection
to be a DBIConnection, why wouldn't you use inheritance?

   setClass("TSconnection", contains="DBIConnection", ...)

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org