[R-es] ERROR: subscript out of bounds

[nuria bs]

Buenas, 

Cuando intento ejecutar el siguiente codigo, me aparece el error " Error in dist.mat[com.names, com.names] : subscript out of bounds". Porque me aparece este error? Y como puedo solucionarlo? 
Gracias!!!

CONSOLE:
> my.phylo<-read.tree("150_BootstrapConsensusTree_Cantabrian_ML.nwk")
> my.sample <- read.delim("C:/Filogenia/my.sample.txt")
> my.sample<-read.table("my.sample.txt",sep="\t", header=T, row.names=1)

> library(SDMTools)

> sntd.a.function <- function(x){
   com.names <- names(x[x > 0])                        # Get de names of the species present in a community
   my.com.dist <- dist.mat[com.names, com.names]       # Distance matrix
   diag(my.com.dist) = NA                              # Diagonal values to NA -> Matriz sim, diagonal zero
   wt.sd(apply(my.com.dist,1,min,na.rm=T), x[x>0])     
 }

> dist.mat<-cophenetic(my.phylo)
> proba<-apply(my.sample, MARGIN = 1, sntd.a.function)

Error in dist.mat[com.names, com.names] : subscript out of bounds 		 	   		  
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