[Rd] [R] type converters not being saved to workspace

[John Chambers]

Well, you  may be right, but my experiments certainly suggested 
otherwise (below).

But my main point is that we should look for a better approach, and I 
think we agree there.

Prof Brian Ripley wrote:

> 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).


Perhaps.  But then why is it that if I put some trace printing in the 
.First.lib of methods, that printing comes out before the message 
"Previously saved  ...."?

> 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).

I'm not disputing that: the methods initialization did not call 
cacheMetaData for the methods package itself--it was because the fix I 
implemented to explicitly cache the generics in methods did NOT work 
that I inferred the point about the ordering.  (Some printout is below, 
but of course I'm not asserting that the fix might not have a different 
problem in it.)

--------------------------
 enterprise:~/testR [160]> R

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ISBN 3-900051-07-0

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cacheMetaData called for methods namespace
[Previously saved workspace restored]

R> names(getMethods("coerce")@methods)
[1] "ANY"      "function"
-----------------------------------
The methods from .GlobalEnv are not found until a second cacheMetaData 
is done.



>
>> 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"
>>>>
>>>>>
>>>>
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>>>>
>>>
>>
>>
>