Error(s) in re-building vignettes:
  ...
--- re-building 'Introduction.Rmd' using rmarkdown

Attaching package: 'iNextPD'

The following object is masked from 'package:iNEXT':

    ggiNEXT

 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
iNextPD
 --- call from context --- 
as.incfreq(x)
 --- call from argument --- 
if (class(x) == "data.frame" | class(x) == "matrix") {
    a <- sort(unique(c(unlist(x))))
    if (!identical(a, c(0, 1))) {
        warning("Invalid data type, the element of species by sites presence-absence matrix should be 0 or 1. Set nonzero elements as 1.")
        x <- (x > 0)
    }
    nT <- ncol(x)
    y <- rowSums(x)
    y <- c(nT, y)
    y
} else if (class(x) == "numeric" | class(x) == "integer" | class(x) == 
    "double") {
    warnings("Ambiguous data type, the input object is a vector. Set total number of sampling units as 1.")
    c(1, x)
} else {
    stop("Invalid data type, it should be a data.frame or matrix.")
}
 --- R stacktrace ---
where 1: as.incfreq(x)
where 2: myFun0(x, U, L, datatype)
where 3: FUN(X[[i]], ...)
where 4: lapply(x, myFun, labels, phy, datatype)
where 5: do.call("rbind", lapply(x, myFun, labels, phy, datatype))
where 6: estPD(x, labels, phy, q = 0, datatype, se = TRUE, conf = conf)
where 7: as.matrix(estPD(x, labels, phy, q = 0, datatype, se = TRUE, conf = conf))
where 8: t(as.matrix(estPD(x, labels, phy, q = 0, datatype, se = TRUE, 
    conf = conf)))
where 9: iNextPD(bird$inci, bird.lab, bird.phy, q = 0, datatype = "incidence_raw", 
    endpoint = 25, se = TRUE)
where 10: eval(expr, envir, enclos)
where 11: eval(expr, envir, enclos)
where 12: withVisible(eval(expr, envir, enclos))
where 13: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 14: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 15: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 16: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 17: evaluate::evaluate(...)
where 18: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), 
    keep_message = !isFALSE(options$message), stop_on_error = if (options$error && 
        options$include) 0L else 2L, output_handler = knit_handlers(options$render, 
        options))
where 19: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 
    stop_on_error = if (options$error && options$include) 0L else 2L, 
    output_handler = knit_handlers(options$render, options)))
where 20: block_exec(params)
where 21: call_block(x)
where 22: process_group.block(group)
where 23: process_group(group)
where 24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 25: process_file(text, output)
where 26: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, 
    encoding = encoding)
where 27: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    ...)
where 28: vweave_rmarkdown(...)
where 29: engine$weave(file, quiet = quiet, encoding = enc)
where 30: doTryCatch(return(expr), name, parentenv, handler)
where 31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 32: tryCatchList(expr, classes, parentenv, handlers)
where 33: 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 34: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/iNextPD.Rcheck/vign_test/iNextPD", 
    ser_elibs = "/tmp/RtmpB0QVME/file2b535c409ae2.rds")

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (x) 
{
    if (class(x) == "data.frame" | class(x) == "matrix") {
        a <- sort(unique(c(unlist(x))))
        if (!identical(a, c(0, 1))) {
            warning("Invalid data type, the element of species by sites presence-absence matrix should be 0 or 1. Set nonzero elements as 1.")
            x <- (x > 0)
        }
        nT <- ncol(x)
        y <- rowSums(x)
        y <- c(nT, y)
        y
    }
    else if (class(x) == "numeric" | class(x) == "integer" | 
        class(x) == "double") {
        warnings("Ambiguous data type, the input object is a vector. Set total number of sampling units as 1.")
        c(1, x)
    }
    else {
        stop("Invalid data type, it should be a data.frame or matrix.")
    }
}
<bytecode: 0x8f540e0>
<environment: namespace:iNextPD>
 --- function search by body ---
Function as.incfreq in namespace iNextPD has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1