Problems with definitions of S4-generics
This isn't a Mac problem, this is a moving from 2.2 to 2.4. You'll probably get better answers on R-devel. My guess would be that a cache used by methods to store frequently used generics isn't getting flushed by removeGeneric properly, though a brief glance at the code suggests that it tries. Your best bet is probably to file a bug report with a simple example.
On 12/21/06, J?rg Beyer <Beyerj at students.uni-marburg.de> wrote:
Hello all,
I installed R 2.4.1 yesterday (coming from 2.2.1), and made an interesting
observation today, which may be a simple coincidence, or related to R 2.4.1.
Platform:
Mac G4/400 PCI (Oct. 1999, PPC-architecture)
Mac OS 10.4.8
R 2.4.1 for Mac OS X (CRAN binary, 2006-12-19) w/ R.app 1.18
Problem-intro:
The file "/Volumes/RAMdisk/beyerjoerg/Scripting R/source-0.R" contains code
that constructs and registers a S4-style generic function, *but only if the
function does not exist, to avoid unnecessary computations.*
This is the stub to test whether or not a S4-Generic is present:
if ( ! isGeneric( <nameOfS4generic> )) {
<setGeneric ...>
}
The code itself has worked without problems with R 2.2.1 -- the code is not
the problem.
Okay, let's start. The function in this example is "cleanDataset"; to
demonstrate the problem, I'm using a second S4-generic here, it is named
"removeFactors".
#### Fist the correct part
## Source the code and build the S4-generic
source( "/Volumes/RAMdisk/beyerjoerg/Scripting R/source-0.R" )
## Do some tests to see if the generic is present, ## and have a look at some details
isGeneric( "cleanDataset" )
[1] TRUE
findFunction( "cleanDataset" )
[[1]] <environment: R_GlobalEnv>
cleanDataset
nonstandardGenericFunction for "cleanDataset" defined from package
".GlobalEnv"
function (object)
{
standardGeneric("cleanDataset")
}
<environment: 0x293bbb8>
Methods may be defined for arguments: object
getGeneric( "cleanDataset" )
## same result as above #### Now what I suspect is a bug ## Delete the S4-generic (and all its methods, if any) ## and repeat the "forensic" test calls
removeGeneric( "cleanDataset" )
[1] TRUE # The following is as expected... ## [I'm trying here to re-translate the message from German back ## to English, so please don't be irritated if there are any differences]
cleanDataset
Error: object "cleanDataset" not found # Oops, but what's that?
getGeneric( "cleanDataset" )
nonstandardGenericFunction for "cleanDataset" defined from package
".GlobalEnv"
function (object)
{
standardGeneric("cleanDataset")
}
<environment: 0x19be228>
Methods may be defined for arguments: object
## Why not try to remove it a second time?
removeGeneric( "cleanDataset" )
[1] FALSE
Warning message:
generic function "cleanDataset" not found for removal in:
removeGeneric("cleanDataset")
# Another test to see if there is a function definition somewhere
# Weird ...
isGeneric( "cleanDataset" )
[1] TRUE # Okay, let's see, where it is # Ah, registered, but nowhere ...
findFunction( "cleanDatasets" )
list() # Just to be sure, test another generic (which I know is *present # and working*) Okay, as expected...
findFunction( "removeFactors" )
[[1]] <environment: R_GlobalEnv> #### Consequence: # Because my code first tests whether a generic is present or not # (see above), re-sourcing the definition code leads to nothing
source( "/Volumes/RAMdisk/beyerjoerg/Scripting R/source-0.R" ) cleanDataset
Error: object "cleanDataset" not found When I skip testing the existence of a generic, everything works as expected, of course. Deleting and redefining generic functions this way never caused problems under R 2.2.1 (I'm developing with this code since six months, the helper functions have been called over and over again), but I don't have explicit results for the above tests and R 2.2.1. Running the above test case in R.app or from the terminal makes no difference. At the moment, I can't see a reason why R should do what it obviously does here, but I may have misunderstood something essential. Some comments may be helpful. Thanks for your interest. Cheers J?rg
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Byron Ellis (byron.ellis at gmail.com) "Oook" -- The Librarian