Error(s) in re-building vignettes:
  ...
--- re-building ‘inference.Rmd’ using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
TDAstats
 --- call from context --- 
permutation_test(unif2d, circle2d, iterations = 100)
 --- call from argument --- 
if (class(data1) != "matrix" | class(data2) != "matrix") {
    stop("Both point clouds must be passed as matrices.")
}
 --- R stacktrace ---
where 1: permutation_test(unif2d, circle2d, iterations = 100)
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)
    }
}, error = function(e) {
    OK <<- FALSE
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 26: tools:::.buildOneVignette("inference.Rmd", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TDAstats.Rcheck/vign_test/TDAstats", 
    TRUE, FALSE, "inference", "UTF-8", "/home/hornik/tmp/scratch/RtmptyZ5e2/file4fd82e85139b.rds")

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (data1, data2, iterations, exponent = 1, update = 0, 
    ...) 
{
    dim <- 1
    list.version <- list(...)
    if (length(list.version) > 0) {
        if (!is.null(list.version$format)) {
            if (list.version$format != "cloud") {
                stop("Permutation tests only work for point clouds.")
            }
        }
        if (!is.null(list.version$dim)) {
            dim <- as.integer(list.version$dim)
        }
    }
    if (update > 0) {
        cat("Starting function\n")
    }
    if (class(data1) != "matrix" | class(data2) != "matrix") {
        stop("Both point clouds must be passed as matrices.")
    }
    if (update > 0) {
        cat("PASSED error check #1\n")
    }
    if (nrow(data1) < 2 | nrow(data2) < 2) {
        stop("Both point clouds must have at least 2 points (rows) each.")
    }
    if (update > 0) {
        cat("PASSED error check #2\n")
    }
    if (ncol(data1) < 2 | ncol(data2) < 2) {
        stop("Both point clouds must be in least 2 dimensions (columns) each.")
    }
    if (update > 0) {
        cat("PASSED error check #3\n")
    }
    if (ncol(data1) != ncol(data2)) {
        stop("Both point clouds must have the same number of dimensions.")
    }
    if (update > 0) {
        cat("PASSED error check #4\n")
    }
    if (sum(is.na(data1)) > 0 | sum(is.na(data2)) > 0) {
        stop("There should be no NAs in the point clouds passed to this function.")
    }
    if (update > 0) {
        cat("PASSED error check #5\n")
    }
    class.data1 <- class(data1[1, 1])
    class.data2 <- class(data2[1, 1])
    allowed.classes <- c("numeric", "integer")
    if (!(class.data1 %in% allowed.classes) | !(class.data2 %in% 
        allowed.classes)) {
        stop("Point clouds must be formatted as matrices filled with integers or numerics.")
    }
    if (update > 0) {
        cat("PASSED error check #6\n")
    }
    if (iterations <= 1) {
        stop("Permutation test must have at least 2 iterations (preferably more).")
    }
    if (update > 0) {
        cat("PASSED error check #7\n")
    }
    if (update > 0) {
        cat("Beginning calculations\n")
    }
    orig.wass <- wass_cloud_calc(data1, data2, exponent, ...)
    if (update > 0) {
        cat("Initial calculation complete; starting iterations\n")
    }
    combo.pts <- rbind(data1, data2)
    wass.values <- matrix(-1, ncol = ncol(data1), nrow = iterations)
    worked <- vapply(X = 1:iterations, FUN.VALUE = logical(1), 
        FUN = function(curr.iter) {
            if (update > 0 & curr.iter%%update == 0) {
                cat("At iteration #", curr.iter, "\n", sep = "")
            }
            curr.pts <- combo.pts[sample.int(n = nrow(combo.pts), 
                size = nrow(combo.pts), replace = FALSE), ]
            curr.wass.calc <- wass_cloud_calc(pts1 = curr.pts[1:nrow(data1), 
                ], pts2 = curr.pts[(nrow(data1) + 1):nrow(curr.pts), 
                ], pow.val = exponent, ...)
            wass.values[curr.iter, ] <<- curr.wass.calc[1:ncol(wass.values)]
            return(TRUE)
        })
    answer <- lapply(X = 0:dim, FUN = function(curr.dim) {
        curr.ans <- list()
        curr.ans$dimension <- curr.dim
        curr.ans$permvals <- wass.values[, curr.dim + 1]
        curr.ans$wasserstein <- orig.wass[curr.dim + 1]
        names(curr.ans$wasserstein) <- NULL
        curr.ans$pvalue <- mean(curr.ans$permvals > curr.ans$wasserstein)
        return(curr.ans)
    })
    if (update > 0) {
        cat("Completed calculations\n")
    }
    return(answer)
}
<bytecode: 0x55f033b7f470>
<environment: namespace:TDAstats>
 --- function search by body ---
Function permutation_test in namespace TDAstats has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
--- re-building ‘inputformat.Rmd’ using rmarkdown
--- finished re-building ‘inputformat.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted