Error(s) in re-building vignettes:
  ...
--- re-building ‘a_introduction.Rmd’ using rmarkdown
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
propr
 --- call from context --- 
propr(ct.k, object@metric, ivar = object@ivar, alpha = object@alpha)
 --- call from argument --- 
if (class(counts) == "data.frame") counts <- as.matrix(counts)
 --- R stacktrace ---
where 1: propr(ct.k, object@metric, ivar = object@ivar, alpha = object@alpha)
where 2: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
where 3: suppressMessages(propr(ct.k, object@metric, ivar = object@ivar, 
    alpha = object@alpha))
where 4: updateCutoffs.propr(object, cutoff)
where 5: updateCutoffs(rho, cutoff = seq(0.05, 0.95, 0.3))
where 6: eval(expr, envir, enclos)
where 7: eval(expr, envir, enclos)
where 8: withVisible(eval(expr, envir, enclos))
where 9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 10: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 12: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 13: evaluate::evaluate(...)
where 14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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 15: 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$render, options)))
where 16: block_exec(params)
where 17: call_block(x)
where 18: process_group.block(group)
where 19: process_group(group)
where 20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 21: process_file(text, output)
where 22: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, 
    encoding = encoding)
where 23: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    ...)
where 24: vweave_rmarkdown(...)
where 25: engine$weave(file, quiet = quiet, encoding = enc)
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: tryCatch({
    engine$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)
    }
}, error = function(e) {
    OK <<- FALSE
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 30: tools:::.buildOneVignette("a_introduction.Rmd", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/propr.Rcheck/vign_test/propr", 
    TRUE, FALSE, "a_introduction", "UTF-8", "/home/hornik/tmp/scratch/RtmprMPqOJ/file701e20fe505e.rds")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (counts, metric = c("rho", "phi", "phs", "cor", "vlr"), 
    ivar = "clr", select, symmetrize = FALSE, alpha, p = 100) 
{
    if (any(counts < 0)) 
        stop("Data may not contain negative measurements.")
    if (any(is.na(counts))) 
        stop("Remove NAs from 'counts' before proceeding.")
    if (class(counts) == "data.frame") 
        counts <- as.matrix(counts)
    if (is.null(colnames(counts))) 
        colnames(counts) <- as.character(1:ncol(counts))
    if (is.null(rownames(counts))) 
        rownames(counts) <- as.character(1:nrow(counts))
    if (missing(alpha)) {
        alpha <- NA
    }
    else {
        if (!is.na(alpha)) 
            if (alpha == 0) 
                alpha <- NA
    }
    ct <- counts
    if (any(as.matrix(counts) == 0) & is.na(alpha)) {
        message("Alert: Replacing 0s with next smallest value.")
        zeros <- ct == 0
        ct[zeros] <- min(ct[!zeros])
    }
    use <- ivar2index(ct, ivar)
    if (is.na(alpha)) {
        message("Alert: Saving log-ratio transformed counts to @logratio.")
        logX <- log(ct)
        logSet <- logX[, use, drop = FALSE]
        ref <- rowMeans(logSet)
        lr <- sweep(logX, 1, ref, "-")
    }
    else {
        message("Alert: Saving alpha transformed counts to @logratio.")
        aX <- (ct^alpha - 1)/alpha
        aSet <- aX[, use, drop = FALSE]
        ref <- rowMeans(aSet)
        lr <- sweep(aX, 1, ref, "-")
    }
    if (!missing(select)) {
        message("Alert: Using 'select' disables permutation testing.")
        p <- 0
        if (!is.vector(select)) 
            stop("Provide 'select' as vector.")
        if (is.character(select)) 
            select <- match(select, colnames(counts))
        if (any(is.na(select))) 
            stop("Some 'select' not in data.")
        counts <- counts[, select]
        ct <- ct[, select]
        lr <- lr[, select]
    }
    lrv <- lr2vlr(lr)
    metric <- metric[1]
    if (metric == "rho") {
        mat <- lr2rho(lr)
    }
    else if (metric == "phi") {
        mat <- lr2phi(lr)
        if (symmetrize) 
            symRcpp(mat)
    }
    else if (metric == "phs") {
        mat <- lr2phs(lr)
    }
    else if (metric == "cor") {
        mat <- stats::cor(lr)
    }
    else if (metric == "vlr") {
        mat <- lrv
    }
    else {
        stop("Provided 'metric' not recognized.")
    }
    result <- new("propr")
    result@counts <- as.data.frame(ct)
    if (!missing(alpha)) {
        result@alpha <- as.numeric(alpha)
    }
    else {
        result@alpha <- as.numeric(NA)
    }
    result@metric <- metric[1]
    result@ivar <- ivar
    result@logratio <- as.data.frame(lr)
    result@pairs <- vector("numeric")
    result@matrix <- mat
    colnames(result@matrix) <- colnames(result@logratio)
    rownames(result@matrix) <- colnames(result@logratio)
    result@permutes <- list(NULL)
    if (p > 0) {
        message("Alert: Fixing permutations to active random seed.")
        permutes <- vector("list", p)
        for (ins in 1:length(permutes)) permutes[[ins]] <- t(apply(ct, 
            1, sample))
        result@permutes <- permutes
    }
    labels <- labRcpp(ncol(lr))
    result@results <- data.frame(Partner = labels[[1]], Pair = labels[[2]], 
        lrv = lltRcpp(lrv), metric = factor(metric), alpha = factor(alpha), 
        propr = lltRcpp(mat))
    if (any(as.matrix(counts) == 0)) {
        message("Alert: Tabulating the presence of 0 counts.")
        result@results$Zeros <- ctzRcpp(as.matrix(counts))
    }
    message("Alert: Use '[' to index proportionality matrix.")
    message("Alert: Use 'updateCutoffs' to calculate FDR.")
    return(result)
}
<bytecode: 0x5653f440d1d0>
<environment: namespace:propr>
 --- function search by body ---
Function propr in namespace propr has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
--- re-building ‘b_visualization.Rmd’ using rmarkdown
Alert: This function ignores index.
Alert: This function ignores index.
Alert: This function ignores index.
Green: Pair positively proportional across all samples.
--- finished re-building ‘b_visualization.Rmd’

--- re-building ‘d_advanced.Rmd’ using rmarkdown
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
--- finished re-building ‘d_advanced.Rmd’

--- re-building ‘e_differential.Rmd’ using rmarkdown
Alert: Fixing permutations to active random seed.
Alert: Use 'setActive' to select a theta type.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Use 'updateF' to calculate F-stat.
Alert: Update FDR or F-stat manually.
Alert: Update FDR or F-stat manually.
--- finished re-building ‘e_differential.Rmd’

--- re-building ‘f_moderation.Rmd’ using rmarkdown
Alert: Fixing permutations to active random seed.
Alert: Use 'setActive' to select a theta type.
Alert: Use 'updateCutoffs' to calculate FDR.
Alert: Use 'updateF' to calculate F-stat.
--- finished re-building ‘f_moderation.Rmd’

--- re-building ‘g_questions.Rmd’ using rmarkdown
--- finished re-building ‘g_questions.Rmd’

SUMMARY: processing the following file failed:
  ‘a_introduction.Rmd’

Error: Vignette re-building failed.
Execution halted