[Phylobase-devl] conversion from ade4 to phylog format: problem

Peter B. Pearman pearman at wsl.ch
Mon Oct 25 14:14:42 CEST 2010

Hello phylobase users and developers,

I've got a little problem that seems strange.  Perhaps one of you can 
enlighten me?

It seems that with updating to R-version 2.12.0 (2010-10-15) the 
following code no longer works:

 >  tree <- 
 > tree$node.label <- paste("node_",as.character(c(410:807)),sep="")
 > phylo4.tree <- as(tree,"phylo4")
 > tree.phylog <- as(phylo4.tree,"phylog")
There were 50 or more warnings (use warnings() to see the first 50)

 > warnings()
Warning messages:
1: In STRING[k] <<- x :
   number of items to replace is not a multiple of replacement length
2: In STRING[k] <<- x :
   number of items to replace is not a multiple of replacement length

(continues ad nauseum)

The node names are all mixed up and there seem to be other problems as well:

 > tree.phylog$nodes
     node_410   node_410_1   node_410_2   node_410_3   node_410_4   
    16.252392     8.929608    24.678913     9.461009     5.245589    
   node_410_6   node_410_7   node_410_8   node_410_9  node_410_10  
    17.960096    15.064738    21.827794     2.024337    49.192003    
  node_410_12  node_410_13  node_410_14  node_410_15  node_410_16  

I re-installed phylobase from source on my MacOS (snow-L 10.6.4), but 
that did not fix the problem.  All phylogenetics and statistical 
packages have been updated.

My office mate ran the same code on his Mac, with R-version:
2.11.1 (2010-5-31)
and a previous binary installation of phylobase.  Everything worked fine 
for him.

I can supply the relevant objects if someone needs to try this on your 

Any help greatly appreciated.



Peter B. Pearman

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