R help - Nov 2011 - Removing or ignoring package version for generic function in locked environment

Hi,

I use the epicalc package which provides the function aggregate.numeric.

Unfortunately aggregate.numeric produces warnings when aggregate is used by
functions not under my control on a numeric value. If I don't load epicalc,
aggregate.default is used instead by these functions and does not produce any
warning.

However I need epicalc. So to get around this, what I would do is firstly remove
aggregate.numeric:

rm(aggregate.numeric, pos=which(search() == "package:epicalc"))

This worked fine in R 2.13.1. However in R 2.14.0 I am getting the following:

Error in rm(aggregate.numeric, pos = which(search() ==
"package:epicalc")) :
  cannot remove bindings from a locked environment

Is there some way I can remove aggregate.numeric, or otherwise prevent it from
being used?

Thanks in advance,

Oliver

Interesting.  I have a few (untested) thoughts.  Before I get into those though,
this seem to me like a case where contacting either the maintainer of epicalc or
of the functions not under your control that give warnings.  I think either
would be appropriate because if the default method works correctly with no
error, I really do not think aggregate.numeric should give a warning.  The onus
seems somewhat on the writer of methods for classes as common as numeric to
write something that works.  That said, without any idea what it is being used
on there are endless possibilities for why a warning is being generated.  But
supposing neither of those are options, here are some ideas.

1) if you happen to be using this in your own package, try just importing
aggregate numeric, rather than fully loading the epicalc package.

2) create a method that mimics aggregate but is for numeric, and make sure it is
in an environment between the out of control functions and epicalc so it is
called rather than epicalcs version.

3) use epicalc and then unload it rather than just removing that function (may
not fly)

4) copy the epicalc aggregate numeric and just use that code  and never load the
package

5) you may be able to unlock() the name space so you can remove the methods (I
think the function is unlock but there may be caps somewhere in there)

6) if the offending functions have a class that is not numeric but inherits from
numeric, you could write a method for their particular class that would then
supersede the inherited numeric method

All of these are highly unsatisfactory in one way another.  I am not in a
position to test anything out at the moment (iPhone, well that's not true, I
could ssh to my cluster, start r there and try via the terminal but that is
truly painful on a phones keyboard)

Good luck,

Josh

On Nov 1, 2011, at 17:31, "Oliver Mannion (COMPASS)" <o.mannion at
auckland.ac.nz> wrote:
> Hi,
> 
> I use the epicalc package which provides the function aggregate.numeric.
> 
> Unfortunately aggregate.numeric produces warnings when aggregate is used by
functions not under my control on a numeric value. If I don't load epicalc,
aggregate.default is used instead by these functions and does not produce any
warning.
> 
> However I need epicalc. So to get around this, what I would do is firstly
remove aggregate.numeric:
> 
> rm(aggregate.numeric, pos=which(search() == "package:epicalc"))
> 
> This worked fine in R 2.13.1. However in R 2.14.0 I am getting the
following:
> 
> Error in rm(aggregate.numeric, pos = which(search() ==
"package:epicalc")) :
>  cannot remove bindings from a locked environment
> 
> Is there some way I can remove aggregate.numeric, or otherwise prevent it
from being used?
> 
> Thanks in advance,
> 
> Oliver
> 
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