Error(s) in re-building vignettes:
  ...
--- re-building ‘popkin.Rmd’ using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
popkin
 --- call from context --- 
popkin(X, subpops)
 --- call from argument --- 
if (class(X) != "function") {
    if (class(X) == "BEDMatrix") {
        n2 <- nrow(X)
    }
    else if (class(X) == "matrix") {
        if (loci_on_cols) {
            n2 <- nrow(X)
        }
        else {
            n2 <- ncol(X)
        }
    }
    else stop("genotype matrix `X` has unsupported class: ", 
        class(X))
    if (n != n2) 
        stop("the length of `subpops` (", n, ") disagrees with the number of individuals in the genotype matrix (", 
            n2, ")")
}
 --- R stacktrace ---
where 1: popkin(X, subpops)
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 9: evaluate::evaluate(...)
where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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 11: 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$render, options)))
where 12: block_exec(params)
where 13: call_block(x)
where 14: process_group.block(group)
where 15: process_group(group)
where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 17: process_file(text, output)
where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, 
    encoding = encoding)
where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    ...)
where 20: vweave_rmarkdown(...)
where 21: engine$weave(file, quiet = quiet, encoding = enc)
where 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, classes, parentenv, handlers)
where 25: tryCatch({
    engine$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 26: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/popkin.Rcheck/vign_test/popkin", 
    ser_elibs = "/home/hornik/tmp/scratch/RtmpuXPQ1j/file1d017a15e1c.rds")

 --- value of length: 2 type: logical ---
[1] TRUE TRUE
 --- function from context --- 
function (X, subpops = NULL, n = NA, loci_on_cols = FALSE, mem_lim = NA, 
    lociOnCols = FALSE, memLim = NA) 
{
    if (lociOnCols && !loci_on_cols) {
        warning("`lociOnCols` is deprecated, please use `loci_on_cols` instead!")
        loci_on_cols <- lociOnCols
    }
    if (!is.na(memLim) && is.na(mem_lim)) {
        warning("`memLim` is deprecated, please use `mem_lim` instead!")
        mem_lim <- memLim
    }
    if (!is.null(subpops)) {
        if (is.na(n)) {
            n <- length(subpops)
        }
        else if (n != length(subpops)) {
            stop("the length of `subpops` (", length(subpops), 
                ") disagreed with the input `n` (", n, ")")
        }
        if (class(X) != "function") {
            if (class(X) == "BEDMatrix") {
                n2 <- nrow(X)
            }
            else if (class(X) == "matrix") {
                if (loci_on_cols) {
                  n2 <- nrow(X)
                }
                else {
                  n2 <- ncol(X)
                }
            }
            else stop("genotype matrix `X` has unsupported class: ", 
                class(X))
            if (n != n2) 
                stop("the length of `subpops` (", n, ") disagrees with the number of individuals in the genotype matrix (", 
                  n2, ")")
        }
    }
    A <- get_A(X, n = n, loci_on_cols = loci_on_cols, mem_lim = mem_lim)
    A_min <- min_mean_subpops(A, subpops)
    kinship <- 1 - A/A_min
}
<bytecode: 0x5583818e3a28>
<environment: namespace:popkin>
 --- function search by body ---
Function popkin in namespace popkin has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1