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"
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Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595