Error(s) in re-building vignettes:
  ...
--- re-building 'vignette.Rnw' using Sweave
Loading required package: rtfbs
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
rtfbs
 --- call from context --- 
label.matrix(x, columnsOnly = TRUE)
 --- 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(x, columnsOnly = TRUE)
where 2: read.pwm("pwm.meme")
where 3: eval(expr, .GlobalEnv)
where 4: eval(expr, .GlobalEnv)
where 5: withVisible(eval(expr, .GlobalEnv))
where 6: doTryCatch(return(expr), name, parentenv, handler)
where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 8: tryCatchList(expr, classes, parentenv, handlers)
where 9: tryCatch(expr, error = function(e) {
    call <- conditionCall(e)
    if (!is.null(call)) {
        if (identical(call[[1L]], quote(doTryCatch))) 
            call <- sys.call(-4L)
        dcall <- deparse(call)[1L]
        prefix <- paste("Error in", dcall, ": ")
        LONG <- 75L
        sm <- strsplit(conditionMessage(e), "\n")[[1L]]
        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
        if (is.na(w)) 
            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 
                type = "b")
        if (w > LONG) 
            prefix <- paste0(prefix, "\n  ")
    }
    else prefix <- "Error : "
    msg <- paste0(prefix, conditionMessage(e), "\n")
    .Internal(seterrmessage(msg[1L]))
    if (!silent && isTRUE(getOption("show.error.messages"))) {
        cat(msg, file = outFile)
        .Internal(printDeferredWarnings())
    }
    invisible(structure(msg, class = "try-error", condition = e))
})
where 10: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 11: evalFunc(ce, options)
where 12: tryCatchList(expr, classes, parentenv, handlers)
where 13: tryCatch(evalFunc(ce, options), finally = {
    cat("\n")
    sink()
})
where 14: driver$runcode(drobj, chunk, chunkopts)
where 15: utils::Sweave(...)
where 16: engine$weave(file, quiet = quiet, encoding = enc)
where 17: doTryCatch(return(expr), name, parentenv, handler)
where 18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 19: tryCatchList(expr, classes, parentenv, handlers)
where 20: tryCatch({
    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)
    if (!have.makefile && vignette_is_tex(output)) {
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
        output <- find_vignette_product(name, by = "texi2pdf", 
            engine = engine)
    }
    outputs <- c(outputs, output)
}, error = function(e) {
    thisOK <<- FALSE
    fails <<- c(fails, file)
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 21: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rtfbs.Rcheck/vign_test/rtfbs", 
    ser_elibs = "/tmp/RtmpimwLdx/file67a02f03023b.rds")

 --- 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: 0x325a1c8>
<environment: namespace:rtfbs>
 --- function search by body ---
Function label.matrix in namespace rtfbs has this body.
 ----------- END OF FAILURE REPORT -------------- 

Error: processing vignette 'vignette.Rnw' failed with diagnostics:
 chunk 1 (label = rarAnalysis1) 
Error in if (class(mat) == "list") { : the condition has length > 1

--- failed re-building 'vignette.Rnw'

SUMMARY: processing the following file failed:
  'vignette.Rnw'

Error: Vignette re-building failed.
Execution halted