Error(s) in re-building vignettes:
  ...
--- re-building ‘autogating_cytometree.Rmd’ using rmarkdown
Loading required package: Rcpp
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
cytometree
 --- call from context --- 
CytomeTree(cellevents, minleaf = 1, t = 0.1)
 --- call from argument --- 
if (class(M) != "matrix" | mode(M) != "numeric") {
    stop("M should be a numeric matrix")
}
 --- R stacktrace ---
where 1: CytomeTree(cellevents, minleaf = 1, t = 0.1)
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("autogating_cytometree.Rmd", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cytometree.Rcheck/vign_test/cytometree", 
    TRUE, FALSE, "autogating_cytometree", "UTF-8", "/home/hornik/tmp/scratch/RtmpZtLM3d/file5986170afdea.rds")

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (M, minleaf = 1, t = 0.1, verbose = TRUE, force_first_markers = NULL) 
{
    if (class(M) == "data.frame") {
        M <- as.matrix(M)
    }
    if (class(M) != "matrix" | mode(M) != "numeric") {
        stop("M should be a numeric matrix")
    }
    n <- nrow(M)
    if (minleaf >= n) {
        stop("minleaf is superior to n.")
    }
    p <- ncol(M)
    if (p > n) {
        stop("p is superior to n.")
    }
    if (any(is.na(M))) {
        stop("M contains NAs.")
    }
    if (is.null(colnames(M))) {
        colnames(M) <- paste0(rep("M", p), 1:p)
    }
    if (!is.null(force_first_markers)) {
        if (any(!(force_first_markers %in% colnames(M)))) {
            cat("'force_first_markers' are not all in M colnames:")
            colnames(M)
            stop()
        }
    }
    BT <- BinaryTree(M, floor(minleaf), t, verbose, force_first_markers)
    annotation <- TreeAnnot(BT$labels, BT$combinations)
    Tree <- list(M = M, labels = BT$labels, pl_list = BT$pl_list, 
        t = t, mark_tree = BT$mark_tree, annotation = annotation)
    class(Tree) <- "CytomeTree"
    return(Tree)
}
<bytecode: 0x55a395aa1f68>
<environment: namespace:cytometree>
 --- function search by body ---
Function CytomeTree in namespace cytometree has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
--- re-building ‘cytoftree.Rmd’ using rmarkdown
Loading required package: Rcpp
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
cytometree
 --- call from context --- 
CytofTree(M = IMdata, minleaf = 1, t = 0.1, verbose = FALSE, 
    force_first_markers = c("(Ir191)Dd_DNA1", "(Ir193)Dd_DNA2", 
        "Cell_length", "(Ce140)Dd_Bead", "(In115)Dd_Dead"), transformation = "asinh", 
    num_col = num_col)
 --- call from argument --- 
if (class(M) == "data.frame") {
    M <- as.matrix(M)
}
 --- R stacktrace ---
where 1: CytofTree(M = IMdata, minleaf = 1, t = 0.1, verbose = FALSE, 
    force_first_markers = c("(Ir191)Dd_DNA1", "(Ir193)Dd_DNA2", 
        "Cell_length", "(Ce140)Dd_Bead", "(In115)Dd_Dead"), transformation = "asinh", 
    num_col = num_col)
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$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("cytoftree.Rmd", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cytometree.Rcheck/vign_test/cytometree", 
    TRUE, FALSE, "cytoftree", "UTF-8", "/home/hornik/tmp/scratch/RtmpZtLM3d/file598634f2a495.rds")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (M, minleaf = 1, t = 0.1, verbose = TRUE, force_first_markers = NULL, 
    transformation = c("asinh", "biexp", "log10", "none"), num_col = 1:ncol(M)) 
{
    if (class(M) == "data.frame") {
        M <- as.matrix(M)
    }
    if (class(M) != "matrix" | mode(M) != "numeric") {
        stop("M should be a numeric matrix")
    }
    n <- nrow(M)
    if (minleaf >= n) {
        stop("minleaf is superior to n.")
    }
    p <- ncol(M)
    if (p > n) {
        stop("p is superior to n.")
    }
    if (any(is.na(M))) {
        stop("M contains NAs.")
    }
    if (is.null(colnames(M))) {
        colnames(M) <- paste0(rep("M", p), 1:p)
    }
    if (!is.null(force_first_markers)) {
        if (any(!(force_first_markers %in% colnames(M)))) {
            cat("'force_first_markers' are not all in M colnames:")
            colnames(M)
            stop()
        }
    }
    if (any(!transformation %in% c("asinh", "biexp", "log10", 
        "none"))) {
        stop("The only allowed values for transformation are 'asinh', 'log10' or 'none'")
    }
    if (length(transformation) > 1) {
        transformation <- transformation[1]
        warning("Default 'asinh' transformation used")
    }
    if (transformation != "none") {
        if (any(!(num_col %in% 1:ncol(M)))) {
            stop(paste0("'num_col' should contain columns indices from 1 to ", 
                ncol(M)))
        }
    }
    else {
        num_col <- NULL
    }
    if (transformation == "asinh") {
        M <- AsinhTransformation(M, num_col)
    }
    if (transformation == "biexp") {
        M <- BiexpTransformation(M, num_col)
    }
    if (transformation == "log10") {
        M <- Log10Transformation(M, num_col)
    }
    BT <- Cytof_BinaryTree(M, floor(minleaf), t, verbose, force_first_markers)
    annotation <- TreeAnnot(BT$labels, BT$combinations)
    Tree <- list(M = M, labels = BT$labels, pl_list = BT$pl_list, 
        t = t, mark_tree = BT$mark_tree, annotation = annotation, 
        transformation = transformation, num_col = num_col)
    class(Tree) <- "CytomeTree"
    cat("It works !", "\n")
    return(Tree)
}
<bytecode: 0x5583547b6328>
<environment: namespace:cytometree>
 --- function search by body ---
Function CytofTree in namespace cytometree has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
SUMMARY: processing the following files failed:
  ‘autogating_cytometree.Rmd’ ‘cytoftree.Rmd’

Error: Vignette re-building failed.
Execution halted