R devel - Aug 2007 - Overriding S4 methods in an installed package

Is it possible to override S4 methods in an installed package?
The naive

library("pkg")
setMethod("foo", signature(obj = "bar"),
        function(obj , x, y) { new definition }
	, where="package:pkg")


results in the error

Error in setMethod("foo", signature(obj = "bar"),
function(obj,  :
        the environment "pkg" is locked; cannot assign methods for
function "foo"

(This is from R 2.5.1 on Fedora Core 5, if that matters)

Background:  A colleague claims to have found an error in a package.
He and I would prefer to do some experimentation before contacting
the authors.  Subclassing is the "correct" way to do this, and I
expect we will eventually subclass for other reasons, but I was
wondering if an override was possible and easier.

Allen McIntosh <mcintosh at research.telcordia.com> writes:
> Is it possible to override S4 methods in an installed package?
> The naive
>
> library("pkg")
> setMethod("foo", signature(obj = "bar"),
>         function(obj , x, y) { new definition }
> 	, where="package:pkg")
>
>
> results in the error
>
> Error in setMethod("foo", signature(obj = "bar"),
function(obj,  :
>         the environment "pkg" is locked; cannot assign methods
for function "foo"
>
> (This is from R 2.5.1 on Fedora Core 5, if that matters)
>
> Background:  A colleague claims to have found an error in a package.
> He and I would prefer to do some experimentation before contacting
> the authors.  Subclassing is the "correct" way to do this, and I
> expect we will eventually subclass for other reasons, but I was
> wondering if an override was possible and easier.
If foo is a generic that you are calling directly, then you can
probably define it in the global environment (omit the where arg) and
test it that way.

OTOH, if foo is used by pkg internally, then it will be much easier to
simply edit the source for pkg, reinstall and test.  If you find and
fix a bug, most package maintainers will be quite happy to integrate
your fix.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/

Seth Falcon wrote:
> Allen McIntosh <mcintosh at research.telcordia.com> writes:
>> Is it possible to override S4 methods in an installed package?
>> The naive
>> library("pkg")
>> setMethod("foo", signature(obj = "bar"),
>>         function(obj , x, y) { new definition }
>> 	, where="package:pkg")
>> results in the error
>> Error in setMethod("foo", signature(obj = "bar"),
function(obj,  :
>>         the environment "pkg" is locked; cannot assign
methods for function "foo"
> 
> If foo is a generic that you are calling directly, then you can
> probably define it in the global environment (omit the where arg) and
> test it that way.
> 
> OTOH, if foo is used by pkg internally, then it will be much easier to
> simply edit the source for pkg, reinstall and test.  If you find and
> fix a bug, most package maintainers will be quite happy to integrate
> your fix.
Thanks for the suggestion.  Unfortunately, foo() uses internal 
functions.  When foo() is defined in the global environment, these are 
not visible.

I was hoping to avoid recompiling and installing under Windows.  Looks 
like I may not have a choice.