[Phylobase-devl] checking readNexus

François Michonneau francois.michonneau at gmail.com
Fri Nov 23 02:13:06 CET 2012

These warnings are generated by NCL as, by default, it only reads strictly
compliant NEXUS files which should include a TAXA block. However, we enable
the option to read "relaxed" NEXUS files that may omit the TAXA block which
generates the warnings. We might be able to silence them if needed. I don't
really have strong feelings either way.

  -- François

On Wed, Nov 21, 2012 at 5:47 PM, Ben Bolker <bbolker at gmail.com> wrote:

>   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?
>   cheers
>     Ben
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