Running examples in ‘rtfbs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build.mm
> ### Title: Build Markov Model to represent sequences in an MS object
> ### Aliases: build.mm
> 
> ### ** Examples
> 
> require("rtfbs")
> exampleArchive <- system.file("extdata", "NRSF.zip", package="rtfbs")
> seqFile <- "input.fas"
> unzip(exampleArchive, seqFile)
> # Read in FASTA file "input.fas" from the examples into an 
> #   MS (multiple sequences) object
> ms <- read.ms(seqFile)
> # Build a 3rd order Markov Model to represent the sequences
> #   in the MS object "ms".  The Model will be a list of
> #   matrices  corrisponding in size to the order of the 
> #   Markov Model
> mm <- build.mm(ms, 3);
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
rtfbs
 --- call from context --- 
label.matrix(mat[[entry]], columnsOnly)
 --- call from argument --- 
if (class(mat) == "list") {
    for (entry in 1:length(mat)) {
        mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
    }
} else if (class(mat) == "matrix") {
    name <- list()
    bases <- list("A", "C", "G", "T")
    if (columnsOnly == FALSE) {
        if (nrow(mat) == 1) {
            name = c("*")
        }
        else {
            for (row in 0:(nrow(mat))) {
                name[row] <- ""
                for (s in 1:log(nrow(mat), 4)) {
                  base <- (ceiling(row/(4^(s - 1)))%%4)
                  if (base == 0) 
                    base <- 4
                  name[row] <- paste(bases[base], name[row], 
                    sep = "")
                }
            }
        }
        rownames(mat) <- name
    }
    colnames(mat) <- bases
}
 --- R stacktrace ---
where 1: label.matrix(mat[[entry]], columnsOnly)
where 2: label.matrix(x)
where 3: build.mm(ms, 3)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (mat, columnsOnly = FALSE) 
{
    check.arg(columnsOnly, "columnsOnly", "logical", null.OK = FALSE)
    if (class(mat) == "list") {
        for (entry in 1:length(mat)) {
            mat[[entry]] <- label.matrix(mat[[entry]], columnsOnly)
        }
    }
    else if (class(mat) == "matrix") {
        name <- list()
        bases <- list("A", "C", "G", "T")
        if (columnsOnly == FALSE) {
            if (nrow(mat) == 1) {
                name = c("*")
            }
            else {
                for (row in 0:(nrow(mat))) {
                  name[row] <- ""
                  for (s in 1:log(nrow(mat), 4)) {
                    base <- (ceiling(row/(4^(s - 1)))%%4)
                    if (base == 0) 
                      base <- 4
                    name[row] <- paste(bases[base], name[row], 
                      sep = "")
                  }
                }
            }
            rownames(mat) <- name
        }
        colnames(mat) <- bases
    }
    mat
}
<bytecode: 0x55dffbfe6610>
<environment: namespace:rtfbs>
 --- function search by body ---
Function label.matrix in namespace rtfbs has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1