R devel - Jun 2003 - R CMD check: is it error to setMethod for class not currently defined?

Should R CMD check consider it an error to define a new method using 
setMethod for a class which is not currently defined? It seems to me that 
it would be best not to consider this an error.

What currently happens in that setMethod issues a warning, quite correctly. 
This warning produces an object 'last.warning'. Then R CMD check issues
a
WARNING that 'last.warning' is an undocumented code object.

Would it be a good idea to make R CMD check disregard the object 
'last.warning' when checking for undocumented code objects? If people 
agree, I could try to make a patch for the R CMD check code.

Gordon

platform i386-pc-mingw32
arch     i386
os       mingw32
system   i386, mingw32
status   Patched
major    1
minor    7.0
year     2003
month    05
day      13
language R

---------------------------------------------------------------------------------------
Dr Gordon K Smyth, Senior Research Scientist, Bioinformatics,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3050, Australia
Tel: (03) 9345 2326, Fax (03) 9347 0852,
Email: smyth@wehi.edu.au, www: http://www.statsci.org

>>>>> Gordon Smyth writes:
> Should R CMD check consider it an error to define a new method using
> setMethod for a class which is not currently defined? It seems to me
> that it would be best not to consider this an error.
[R CMD check by itself definitely does not test for this.]
> What currently happens in that setMethod issues a warning, quite
> correctly.  This warning produces an object 'last.warning'. Then R
CMD
> check issues a WARNING that 'last.warning' is an undocumented code
> object.
> Would it be a good idea to make R CMD check disregard the object
> 'last.warning' when checking for undocumented code objects? If
people
> agree, I could try to make a patch for the R CMD check code.
Why should it?  Packages could have an object called last.warning in
their environment---the last.warning created by warning() seems to end
up in .GlobalEnv ...

What seems to happen is that you have a package installed as a save
image which at save time creates a warning and hence last.warning in
.GlobalEnv.  The way installing as a save image works everything in
.GlobalEnv gets included in the package environment.  If for some reason
this produces something 'unwanted', it can still be removed e.g. from
inside the package load hook(s) (e.g., your .First.lib()).  The QC
tools, when working on installed packages, simply load and attach them,
and perform computations on what is available then.

Best
-k

At 04:37 PM 9/06/2003, you wrote:
> >>>>> Gordon Smyth writes:
>
> > Should R CMD check consider it an error to define a new method using
> > setMethod for a class which is not currently defined? It seems to me
> > that it would be best not to consider this an error.
>
>[R CMD check by itself definitely does not test for this.]
>
> > What currently happens in that setMethod issues a warning, quite
> > correctly.  This warning produces an object 'last.warning'.
Then R CMD
> > check issues a WARNING that 'last.warning' is an undocumented
code
> > object.
>
> > Would it be a good idea to make R CMD check disregard the object
> > 'last.warning' when checking for undocumented code objects? If
people
> > agree, I could try to make a patch for the R CMD check code.
>
>Why should it?  Packages could have an object called last.warning in
>their environment---the last.warning created by warning() seems to end
>up in .GlobalEnv ...
>
>What seems to happen is that you have a package installed as a save
>image which at save time creates a warning and hence last.warning in
>.GlobalEnv.  The way installing as a save image works everything in
>.GlobalEnv gets included in the package environment.  If for some reason
>this produces something 'unwanted', it can still be removed e.g.
from
>inside the package load hook(s) (e.g., your .First.lib()).  The QC
>tools, when working on installed packages, simply load and attach them,
>and perform computations on what is available then.
Thanks for this. Including the code 'rm(last.warning)' in the right
place
solves the problem.

Gordon
>Best
>-k