[Phylobase-devl] Urgent! problems with installing
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.
> 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:
if (translation) semico[semico > i2] + 1
else semico[semico > i1]
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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