Error(s) in re-building vignettes:
  ...
--- re-building 'neat.Rmd' using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
neat
 --- call from context --- 
neat(alist = induced_genes, blist = functional_sets, network = yeast$yeastnet, 
    nettype = "undirected", nodes = yeast$ynetgenes, alpha = 0.01)
 --- call from argument --- 
if (class(network) == "igraph") {
    requireNamespace("igraph", quietly = TRUE)
    net = networkmatrix(network, nodes, nettype)
} else if (class(network) == "matrix" & ncol(network) > 2) {
    if (isSymmetric(network) == TRUE & nettype == "directed") {
        warning("The adjacency matrix is symmetric. Should you set nettype = \"undirected\"?")
    }
    if (isSymmetric(network) == FALSE & nettype == "undirected") {
        warning("The adjacency matrix is not symmetric. Should you set nettype = \"directed\"?")
    }
    net = networkmatrix(network, nodes, nettype)
} else if (class(network) == "dgCMatrix") {
    requireNamespace("Matrix", quietly = TRUE)
    net = networkmatrix(network, nodes, nettype)
} else if (class(network) == "matrix" & ncol(network) == 2) net = network
 --- R stacktrace ---
where 1: neat(alist = induced_genes, blist = functional_sets, network = yeast$yeastnet, 
    nettype = "undirected", nodes = yeast$ynetgenes, alpha = 0.01)
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)
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-clang/Work/PKGS/neat.Rcheck/vign_test/neat", 
    ser_elibs = "/tmp/Rtmp0h35RN/file5f05155f509.rds")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (alist, blist = NULL, network, nettype, nodes, alpha = NULL, 
    anames = NULL, bnames = NULL) 
{
    if (is.null(alpha) == FALSE) {
        if (alpha <= 0 | alpha >= 1) 
            stop("alpha must be in (0,1)")
    }
    if ((nettype %in% c("directed", "undirected")) == FALSE) 
        stop("nettype must be either 'directed' or 'undirected' ")
    if (nettype == "directed" & is.null(blist)) 
        stop("blist cannot be null when nettype == 'directed' (see manual)")
    if (class(network) == "igraph") {
        requireNamespace("igraph", quietly = TRUE)
        net = networkmatrix(network, nodes, nettype)
    }
    else if (class(network) == "matrix" & ncol(network) > 2) {
        if (isSymmetric(network) == TRUE & nettype == "directed") {
            warning("The adjacency matrix is symmetric. Should you set nettype = \"undirected\"?")
        }
        if (isSymmetric(network) == FALSE & nettype == "undirected") {
            warning("The adjacency matrix is not symmetric. Should you set nettype = \"directed\"?")
        }
        net = networkmatrix(network, nodes, nettype)
    }
    else if (class(network) == "dgCMatrix") {
        requireNamespace("Matrix", quietly = TRUE)
        net = networkmatrix(network, nodes, nettype)
    }
    else if (class(network) == "matrix" & ncol(network) == 2) 
        net = network
    if (is.factor(nodes) == T) {
        nodes = as.character(nodes)
    }
    oa = numeric()
    ib = numeric()
    nab = numeric()
    alogic = vector("list", length(alist))
    netred = vector("list", length(alist))
    p = numeric()
    expect = numeric()
    o = vector()
    concl = vector()
    from = vector()
    to = vector()
    if (nettype == "undirected") {
        eina = vector("list", length(alist))
        alogic2 = alogic
        if (is.null(names(alist))) 
            names(alist) = anames
        for (i in 1:length(alist)) {
            if (is.factor(alist[[i]]) == T) {
                alist[[i]] = as.character(alist[[i]])
            }
            eina[[i]] = (net[, 1] %in% alist[[i]]) | (net[, 2] %in% 
                alist[[i]])
            if (sum(eina[[i]]) == 1) 
                netred[[i]] = as.matrix(t(net[eina[[i]], ]))
            else if (sum(eina[[i]]) == 0) 
                stop(paste("There are no edges connected to genes in", 
                  names(alist)[i], ". The test cannot be computed."))
            else netred[[i]] = net[eina[[i]], ]
            alogic[[i]] = (netred[[i]][, 1] %in% alist[[i]])
            alogic2[[i]] = (netred[[i]][, 2] %in% alist[[i]])
            oa[i] = sum(alogic[[i]]) + sum(alogic2[[i]])
        }
        if (is.null(blist) == FALSE) {
            blogic = vector("list", length(blist))
            blogic2 = blogic
            einb = vector("list", length(blist))
            if (is.null(names(blist))) 
                names(blist) = bnames
            for (i in 1:length(blist)) {
                if (is.factor(blist[[i]]) == T) {
                  blist[[i]] = as.character(blist[[i]])
                }
                einb[[i]] = (net[, 1] %in% blist[[i]]) | (net[, 
                  2] %in% blist[[i]])
                if (sum(einb[[i]]) == 0) 
                  stop(paste("There are no edges connected to genes in", 
                    names(blist)[i], ". The test cannot be computed."))
                else if (sum(einb[[i]]) == 1) {
                  temp = as.matrix(t(net[einb[[i]], ]))
                  blogic[[i]] = (temp[, 1] %in% blist[[i]])
                  blogic2[[i]] = (temp[, 2] %in% blist[[i]])
                }
                else {
                  blogic[[i]] = (net[einb[[i]], ][, 1] %in% blist[[i]])
                  blogic2[[i]] = (net[einb[[i]], ][, 2] %in% 
                    blist[[i]])
                }
                ib[i] = sum(blogic[[i]]) + sum(blogic2[[i]])
            }
            k = 1
            for (i in 1:length(alist)) {
                for (j in 1:length(blist)) {
                  from[k] = names(alist)[i]
                  to[k] = names(blist)[j]
                  link = (alogic[[i]] & netred[[i]][, 2] %in% 
                    blist[[j]]) | (alogic2[[i]] & netred[[i]][, 
                    1] %in% blist[[j]])
                  nab[k] = sum(link)
                  temp = pvalue(nab[k], ss = oa[i], K = ib[j], 
                    N = 2 * dim(net)[1])
                  p[k] = temp$p
                  expect[k] = round(ib[j] * oa[i]/(2 * dim(net)[1]), 
                    4)
                  o[k] = temp$overenr
                  if (is.null(alpha) == FALSE) {
                    if (p[k] > alpha) 
                      concl[k] = "No enrichment"
                    else if (p[k] <= alpha & o[k] == T) 
                      concl[k] = "Overenrichment"
                    else if (p[k] <= alpha & o[k] == F) 
                      concl[k] = "Underenrichment"
                  }
                  k = k + 1
                }
            }
        }
        if (is.null(blist) == TRUE) {
            ib = oa
            k = 1
            for (i in 1:(length(alist) - 1)) {
                for (j in (i + 1):length(alist)) {
                  from[k] = names(alist)[i]
                  to[k] = names(alist)[j]
                  link = (alogic[[i]] & netred[[i]][, 2] %in% 
                    alist[[j]]) | (alogic2[[i]] & netred[[i]][, 
                    1] %in% alist[[j]])
                  nab[k] = sum(link)
                  temp = pvalue(nab[k], ss = oa[i], K = ib[j], 
                    N = 2 * dim(net)[1])
                  p[k] = temp$p
                  expect[k] = round(ib[j] * oa[i]/(2 * dim(net)[1]), 
                    4)
                  o[k] = temp$overenr
                  if (is.null(alpha) == FALSE) {
                    if (p[k] > alpha) 
                      concl[k] = "No enrichment"
                    else if (p[k] <= alpha & o[k] == T) 
                      concl[k] = "Overenrichment"
                    else if (p[k] <= alpha & o[k] == F) 
                      concl[k] = "Underenrichment"
                  }
                  k = k + 1
                }
            }
        }
    }
    if (nettype == "directed") {
        if (is.null(names(alist))) 
            names(alist) = anames
        for (i in 1:length(alist)) {
            if (is.factor(alist[[i]]) == T) {
                alist[[i]] = as.character(alist[[i]])
            }
            alogic[[i]] = (net[, 1] %in% alist[[i]])
            oa[i] = sum(alogic[[i]])
            if (sum(alogic[[i]]) == 1) 
                netred[[i]] = as.matrix(t(net[alogic[[i]], ]))
            else if (sum(alogic[[i]]) == 0) 
                stop(paste("There are no arrows going out from genes in", 
                  names(alist)[i]), ". The test cannot be computed.")
            else netred[[i]] = net[alogic[[i]], ]
        }
        if (is.null(blist) == FALSE) {
            blogic = vector("list", length(blist))
            if (is.null(names(blist))) 
                names(blist) = bnames
            for (i in 1:length(blist)) {
                if (is.factor(blist[[i]]) == T) {
                  blist[[i]] = as.character(blist[[i]])
                }
                blogic[[i]] = (net[, 2] %in% blist[[i]])
                ib[i] = sum(blogic[[i]])
            }
            k = 1
            for (i in 1:length(alist)) {
                for (j in 1:length(blist)) {
                  from[k] = names(alist)[i]
                  to[k] = names(blist)[j]
                  nab[k] = sum(netred[[i]][, 2] %in% blist[[j]])
                  temp = pvalue(nab[k], ss = oa[i], K = ib[j], 
                    N = dim(net)[1])
                  p[k] = temp$p
                  expect[k] = round(ib[j] * oa[i]/dim(net)[1], 
                    4)
                  o[k] = temp$overenr
                  if (is.null(alpha) == FALSE) {
                    if (p[k] > alpha) 
                      concl[k] = "No enrichment"
                    else if (p[k] <= alpha & o[k] == T) 
                      concl[k] = "Overenrichment"
                    else if (p[k] <= alpha & o[k] == F) 
                      concl[k] = "Underenrichment"
                  }
                  k = k + 1
                }
            }
        }
    }
    if (is.null(alpha) == FALSE) {
        results = data.frame(from, to, nab, expect, p, concl)
        names(results) = c("A", "B", "nab", "expected_nab", "pvalue", 
            "conclusion")
    }
    else {
        results = data.frame(from, to, nab, expect, p)
        names(results) = c("A", "B", "nab", "expected_nab", "pvalue")
    }
    class(results) = c("neat", "data.frame")
    results
}
<bytecode: 0x3dbee10>
<environment: namespace:neat>
 --- function search by body ---
Function neat in namespace neat has this body.
 ----------- END OF FAILURE REPORT -------------- 
Quitting from lines 77-79 (neat.Rmd) 
Error: processing vignette 'neat.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'neat.Rmd'

SUMMARY: processing the following file failed:
  'neat.Rmd'

Error: Vignette re-building failed.
Execution halted