[Phylobase-devl] checking readNexus

Ben Bolker bbolker at gmail.com
Wed Nov 21 23:47:16 CET 2012

  I have been fussing with phylobase, and I think it's basically ready
to go, but I have a question for someone more knowledgeable than I am
about Nexus reading.

  We are getting a lot of warnings of this type:

 A TAXA block should be read before the TREES block (but no TAXA block
was found).  Taxa will be inferred from their usage in the TREES block.
at line 8, column (approximately) 9 (file position 217)
storing implied block: TAXA
storing read block: TREES

  you can look at tests/doRUnit.Rout.save to see examples.

  Can anyone say whether these are effectively false positives that
should be suppressed?


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