Running examples in 'picante-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: comdist
> ### Title: Calculates inter-community mean pairwise distance
> ### Aliases: comdist
> ### Keywords: univar
> 
> ### ** Examples
> 
> data(phylocom)
> comdist(phylocom$sample, cophenetic(phylocom$phylo), abundance.weighted=TRUE)
[1] "Dropping taxa from the distance matrix because they are not present in the community data:"
[1] "sp16" "sp23" "sp27" "sp28" "sp30" "sp31" "sp32"
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
picante
 --- call from context --- 
match.comm.dist(comm, dis)
 --- call from argument --- 
if (disclass == "dist") {
    res$dist <- as.dist(dis[colnames(comm), colnames(comm)])
} else {
    res$dist <- dis[colnames(comm), colnames(comm)]
}
 --- R stacktrace ---
where 1: match.comm.dist(comm, dis)
where 2: comdist(phylocom$sample, cophenetic(phylocom$phylo), abundance.weighted = TRUE)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (comm, dis) 
{
    res <- list()
    commtaxa <- colnames(comm)
    if (is.null(commtaxa)) {
        stop("Community data set lacks taxa (column) names, these are required to match distance matrix and community data")
    }
    disclass <- class(dis)
    dis <- as.matrix(dis)
    distaxa <- rownames(dis)
    if (is.null(distaxa)) {
        warning("Distance matrix lacks taxa names, these are required to match community and distance matrix. Data are returned unsorted. Assuming that distance matrix and community data taxa columns are in the same order!")
        if (disclass == "dist") {
            return(list(comm = comm, dist = as.dist(dis)))
        }
        else {
            return(list(comm = comm, dist = dis))
        }
    }
    if (!all(distaxa %in% commtaxa)) {
        print("Dropping taxa from the distance matrix because they are not present in the community data:")
        print(setdiff(distaxa, commtaxa))
        dis <- dis[intersect(distaxa, commtaxa), intersect(distaxa, 
            commtaxa)]
        distaxa <- rownames(dis)
    }
    if (any(!(commtaxa %in% distaxa))) {
        print("Dropping taxa from the community because they are not present in the distance matrix:")
        print(setdiff(commtaxa, distaxa))
        res$comm <- comm[, intersect(commtaxa, distaxa)]
    }
    else {
        res$comm <- comm
    }
    if (disclass == "dist") {
        res$dist <- as.dist(dis[colnames(comm), colnames(comm)])
    }
    else {
        res$dist <- dis[colnames(comm), colnames(comm)]
    }
    return(res)
}
<bytecode: 0xba4d618>
<environment: namespace:picante>
 --- function search by body ---
Function match.comm.dist in namespace picante has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (disclass == "dist") { : the condition has length > 1
Calls: comdist -> match.comm.dist
Execution halted