type converters not being saved to workspace

On Tue, 11 Apr 2006, John Chambers wrote:

(diverted to r-devel)

The problem seems to be rather that loading of the saved image takes 
place _after_ the packages are attached.  So nothing that the methods 
package does in its initialization will see the relevant type 
converters or other methods objects.

I am sorry, but that is not the case: see ?Startup. The image is 
loaded _before_ the packages are attached (as documented).

You can check explicitly by

env R_DEFAULT_PACKAGES=NULL R --restore
# R starts and loads the workspace

library(methods)

and it still does not work (as I had tried before answering).

More generally, loading into .GlobalEnv will never cause the 
equivalent of cacheMetaData(.GlobalEnv).

It would be possible to hack the C code in main/saveload.c to 
generate a call to cacheMetaData under the right circumstances, but 
is that the best solution? Intuitively, it's the objects containing 
the method/class definitions that should trigger actions when they 
are loaded (emulating what happens when the corresponding setMethod 
or setClass function call takes place).  I.e., a load method for 
these classes of objects.  Possible?

Yes, but it will not help here as the objects are loaded without 
methods being loaded.

I hope one day when we have S4 objects marked in the object headers 
that loading such an object will load and attach the methods package.

It might be better, now that we're past feature freeze, to leave this 
as a "design infelicity" for the upcoming release.

Definitely.

I think that package methods needs to cache metadata in its .onAttach 
not .onLoad.  In principle it affects anything setting methods for 
generics in package:methods, but if this is done in a package, the 
dependency on methods will ensure that methods is loaded before the 
package, and then library() will run cacheMetaData on the package.

Prof Brian Ripley wrote:

It is recommended that you use a package for this sort of thing.

When a package is loaded, the S4 methods it contains are merged into 
the metadata.  When the global environment is loaded, they are not.  
Call 'cacheMetaData(1)' to do so.

[This looks like a bug: cacheMetaData is called on .GlobalEnv in the 
startup code for package methods, but seems not to work when called 
from there.  I think this is because package methods is not at that 
point on the search path (the call is from .onLoad) and hence the 
coerce() generic is not visible to cacheMetaData.  If you have S4 
code in a package, it will ensure that package methods is attached 
before your package is loaded.]

On Sun, 9 Apr 2006, Joseph Wang wrote:

Any one can explain why this happens or any work arounds?

setClass('foo')

[1] "foo"

setAs('foo', 'character', function(from) from)
showMethods('coerce')

Function "coerce":
from = "ANY", to = "array"
from = "ANY", to = "call"
from = "ANY", to = "character"
from = "ANY", to = "complex"
from = "ANY", to = "environment"
from = "ANY", to = "expression"
from = "ANY", to = "function"
from = "ANY", to = "integer"
from = "ANY", to = "list"
from = "ANY", to = "logical"
from = "ANY", to = "matrix"
from = "ANY", to = "name"
from = "ANY", to = "numeric"
from = "ANY", to = "single"
from = "ANY", to = "ts"
from = "ANY", to = "vector"
from = "ANY", to = "NULL"
from = "foo", to = "character"

q()

Save workspace image? [y/n/c]: y


(restart)

showMethods('coerce')

Function "coerce":
from = "ANY", to = "array"
from = "ANY", to = "call"
from = "ANY", to = "character"
from = "ANY", to = "complex"
from = "ANY", to = "environment"
from = "ANY", to = "expression"
from = "ANY", to = "function"
from = "ANY", to = "integer"
from = "ANY", to = "list"
from = "ANY", to = "logical"
from = "ANY", to = "matrix"
from = "ANY", to = "name"
from = "ANY", to = "numeric"
from = "ANY", to = "single"
from = "ANY", to = "ts"
from = "ANY", to = "vector"
from = "ANY", to = "NULL"
from = "NULL", to = "OptionalFunction"