R devel - Jul 2009 - Handling masked methods

Hi,

Say I have two packages, test1 and test2, that both define the generic 
method train (identical definition), and each has a specific train 
method for a different S4 object (foo and bar, resp.)

I want to be able to call train(foo, x, y) and train(bar, x, y), which 
doesn't work since test2 masks test1, as seen below.

The two solutions I can think of are to a) prefix train, 
test1::train(foo) and test2::train(bar), which gets cumbersome for 
non-trivial code, or b) make test2 depend on test1 so it doesn't have to 
define the generic, but I'd rather keep the packages compatible but not 
dependent. Any suggestions?

You can get the code at
http://www.cs.mu.oz.au/~gabraham/test1_0.1.tar.gz
and
http://www.cs.mu.oz.au/~gabraham/test2_0.1.tar.gz

Thanks,
Gad

 > library(test1)
 > f <- new('foo')
 > f
An object of class ?foo?
Slot "x":
      [,1]
[1,]   NA

Slot "y":
logical(0)

 > x <- matrix(rnorm(9), 3, 3)
 > y <- rnorm(3)
 > train(f, x, y)
An object of class ?foo?
Slot "x":
            [,1]       [,2]      [,3]
[1,] -1.1274528  1.5079401 1.5252550
[2,] -1.8574282  0.1638099 0.4446156
[3,] -0.7004087 -0.6221687 2.2455707

Slot "y":
[1] -0.2074759  0.2224259  1.1194120

 > library(test2)

Attaching package: 'test2'


	The following object(s) are masked from package:test1 :

	 train

 > train(f, x, y)
Error in function (classes, fdef, mtable)  :
   unable to find an inherited method for function "train", for 
signature "foo", "matrix", "numeric"
 > test2::train
standardGeneric for "train" defined from package "test2"

function (object, x, y, ...)
standardGeneric("train")
<environment: 0x160a22d0>
Methods may be defined for arguments: object, x, y
Use  showMethods("train")  for currently available ones.
 > test1::train
standardGeneric for "train" defined from package "test1"

function (object, x, y, ...)
standardGeneric("train")
<environment: 0x16075070>
Methods may be defined for arguments: object, x, y
Use  showMethods("train")  for currently available ones.

-- 
Gad Abraham
MEng Student, Dept. CSSE and NICTA
The University of Melbourne
Parkville 3010, Victoria, Australia
email: gabraham at csse.unimelb.edu.au
web: http://www.csse.unimelb.edu.au/~gabraham

Gad Abraham wrote:
> Hi,
>
> Say I have two packages, test1 and test2, that both define the generic 
> method train (identical definition), and each has a specific train 
> method for a different S4 object (foo and bar, resp.)
>
> I want to be able to call train(foo, x, y) and train(bar, x, y), which 
> doesn't work since test2 masks test1, as seen below.
>
> The two solutions I can think of are to a) prefix train, 
> test1::train(foo) and test2::train(bar), which gets cumbersome for 
> non-trivial code, or b) make test2 depend on test1 so it doesn't have
to
> define the generic, but I'd rather keep the packages compatible but not
> dependent. Any suggestions?
>
>   
Two other possibilities:

Make just one package, with just one definition, and put all the other 
stuff from test1 and test2 into it.

Make a third package to hold the generic, and have both packages depend 
on that.

Duncan Murdoch
> You can get the code at
> http://www.cs.mu.oz.au/~gabraham/test1_0.1.tar.gz
> and
> http://www.cs.mu.oz.au/~gabraham/test2_0.1.tar.gz
>
> Thanks,
> Gad
>
>  > library(test1)
>  > f <- new('foo')
>  > f
> An object of class ?foo?
> Slot "x":
>       [,1]
> [1,]   NA
>
> Slot "y":
> logical(0)
>
>  > x <- matrix(rnorm(9), 3, 3)
>  > y <- rnorm(3)
>  > train(f, x, y)
> An object of class ?foo?
> Slot "x":
>             [,1]       [,2]      [,3]
> [1,] -1.1274528  1.5079401 1.5252550
> [2,] -1.8574282  0.1638099 0.4446156
> [3,] -0.7004087 -0.6221687 2.2455707
>
> Slot "y":
> [1] -0.2074759  0.2224259  1.1194120
>
>  > library(test2)
>
> Attaching package: 'test2'
>
>
> 	The following object(s) are masked from package:test1 :
>
> 	 train
>
>  > train(f, x, y)
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function "train", for 
> signature "foo", "matrix", "numeric"
>  > test2::train
> standardGeneric for "train" defined from package
"test2"
>
> function (object, x, y, ...)
> standardGeneric("train")
> <environment: 0x160a22d0>
> Methods may be defined for arguments: object, x, y
> Use  showMethods("train")  for currently available ones.
>  > test1::train
> standardGeneric for "train" defined from package
"test1"
>
> function (object, x, y, ...)
> standardGeneric("train")
> <environment: 0x16075070>
> Methods may be defined for arguments: object, x, y
> Use  showMethods("train")  for currently available ones.
>
>