[Phylobase-devl] Urgent! problems with installing

Brian O'Meara bcomeara at nescent.org
Wed Jul 2 16:56:27 CEST 2008

On Jul 2, 2008, at 9:19 AM, Marguerite Butler wrote:

> Here is the nexus file that read.nexus couldn't read under R 2.7.1  
> yesterday (this was a problem both for macs and pc's on several  
> people's computers -- I had a small group of students try it). When  
> I downgraded it read in fine.
> <squamatetree1.nex>
> It would be great if you could give it a try.

I have a Mac with 10.4.11, R version 2.7.1, ape version 2.2  
(installed from source), phylobase revision 192. read.nexus gave the  
error 'Error in read.nexus("squamatetree1.nex") : object "TRANS" not  
found', which is odd because the tree file does not have a translate  
block (TRANS only occurs where translation=true). If instead you run  
read.nexus line by line, it gives an error here:

start <-
        if (translation) semico[semico > i2][1] + 1
          else semico[semico > i1][1]

Error: syntax error

Note that loading read.nexus line by line results in translation  
being set correctly to false (before the above syntax error occurs).

NexusToPhylo4, which uses some of read.nexus' code, doesn't throw an  
error, but the loaded tree seems to be wrong (some nodes are labeled  
internal yet have taxon names; plotting didn't work on the tree object).

FigTree, a Java tree-plotting program, opens and displays the tree  
fine, so I don't think the problem's in the file.


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