I overlooked blogging about this at the time, but Jari released a minor update to our Vegan package to fix a few issues following release of R 2.13-0. As far as the user is concerned, this mainly affects capscale(). metaMDSrotate(), a helper function for rotating nMDS solutions from function metaMDS() can now handle missing values via argument na.rm = TRUE. The relevant section of the NEWS file is reproduced below.

                   CHANGES IN VEGAN 1.17-10

    - This is minor revision that mainly fixes vegan with respect to
      changes in the currently released R 2.13.0. Most importantly,
      cmdscale() output changed in R 2.13.0 and because of this
      capscale() could fail in some rare situations with argument 'add
      = TRUE'. This vegan bug made BiodiversityR package fail its
      tests in R 2.13.0. 

    - metaMDSrotate: gained argument na.rm = TRUE.


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