[R-sig-eco] Package bio.infer: get.taxonomic() hangs R after editing taxa list

[Rich Shepard]

On Mon, 10 Dec 2012, Sarah Goslee wrote:

> ... get.taxonomic() no longer has an outputFile argument.

   I've read the get.taxonomic() description in bio.infer.pdf and it works
... to a point. There are 3 taxa currently not in the ITIS database (a
freshwater worm, a midge, and one chironomid for which I can't track down
the genus). The first two are going through the validation process and will
be added to ITIS Real Soon Now. In the meantime, I don't know how to
proceed. So I've copied Lester Yuan on this message.

   I tell get.taxonomic() that I'm finished editing and it flashes a Tcl/Tk
window then ists the taxa not in the data base, but does not return the R
prompt:

> jerall <- get.taxonomic(bioinfer)
The following taxa are not in ITIS:
EISENIELLA
RADOTANYPUS
ZIATZEVIA

   I've not found a key combination that lets me gracefully exit R (or emacs
for that matter); I can only kill the process. Nothing I've seen in the help
files appears relevant.

   Any suggestions?

Rich