If I run "R CMD check" on my package source directory I get no warnings 
(okay, at the moment I get a few, but lets imagine for the sake of 
argument I don't). Then if I run it again I get a warning about my 
source package having object files in it:

* checking if this is a source package ... WARNING
Subdirectory 'foo/src' contains object files.

  Well, I didn't put them there!

  Can't find anyone else really griping about this on the R search 
stuff. So am I doing something wrong?

  Is there a standard way I can do a 'clean' in the source subdirectory 
before the check?

  Thanks in advance for any ideas, I'm really just putting off sorting 
out the code/documentation warnings...

Barry

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