[Phylobase-devl] New phylobase build approach using static libncl (Was: Rcpp and OS X compiliation)

[François Michonneau]

Hi,

  Ouch! We need to fix this.

  There might be some hope if we use Rcpp to build the data frame
instead of building and parsing a string.

  Let me talk to Dirk about it and see what we can do.

  Cheers,
  -- François

On Fri, 2010-04-23 at 13:59 +0100, Orme, David wrote:
> Hi all,
> 
> From an e-mail on 03/03/10:
> 
> Mark then Peter
> 
> >> The main potential problems that I see with the ways that phylobase is using NCL now are:
> >> 	1. in NCLInterface.cpp there are lots of call to RemoveUnderscoresAndSpaces to get rid of spaces and _ in names.  That makes names easier to deal with, but at some point will bite you (somebody will have dataset with a taxon labelled "AB" and another with "A B", after transformation there will be a name clash).
> > 
> > I agree that this is something to address.  Not only might there be clashes but changing names, will be annoying to users.  Brian or Derrick could answer better, but I assume this is because some of the code used to parse the tree string can't handle the underscores and spaces.
> 
> Has just bitten me! There is a deeper problem here in that readNexus uses the NCLInterface code to get the data frame as parsable R code - with stripped spaces and underscores - but the tree block is passed over as a block of raw text from the file. These names _aren't_ then stripped of underscores and spaces by read.nexustreestring() and so the name checking throws an error. 
> 
> Obviously there is an ongoing deeper discussion about how to handle passing the tree from NCL and how to handle the dismayingly wide range of official valid PAUP identifiers using regex but currently we've got a simpler problem of different handling. Underscores in names are very commonly used to avoid the quoting problem with spaces so I think this current problem will come up a lot. 
> 
> Cheers,
> David
> 
> 
> 
> 
> 
> 
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