Error(s) in re-building vignettes:
  ...
--- re-building ‘functional_prediction.Rmd’ using rmarkdown
--- finished re-building ‘functional_prediction.Rmd’

--- re-building ‘thematic_structure.Rmd’ using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
themetagenomics
 --- call from context --- 
create_multiclasses_table(estimated_effects$modelframe, estimated_effects$modelframe_full, 
    spline_idx)
 --- call from argument --- 
if (class(multiclasses) == "list") {
    out <- cbind(full = names(sapply(modelframe_full, class)), 
        do.call("rbind", multiclasses))
    rownames(out) <- NULL
} else {
    out <- cbind(colnames(modelframe_full), t(multiclasses))
    colnames(out) <- c("full", "baseclass", "multiclass", "lev", 
        "ref")
    rownames(out) <- NULL
}
 --- R stacktrace ---
where 1: create_multiclasses_table(estimated_effects$modelframe, estimated_effects$modelframe_full, 
    spline_idx)
where 2: est_topics_backend(estimated_effects, fit$theta, nsims = nsims, 
    ui_level = ui_level, npoints = npoints, verbose = verbose)
where 3: est.topics(TOPICS)
where 4: est(TOPICS)
where 5: system.time(TOPIC_EFFECTS <- est(TOPICS))
where 6: eval(expr, envir, enclos)
where 7: eval(expr, envir, enclos)
where 8: withVisible(eval(expr, envir, enclos))
where 9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 10: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 12: evaluate_call(expr, parsed$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("thematic_structure.Rmd", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/themetagenomics.Rcheck/vign_test/themetagenomics", 
    TRUE, FALSE, "thematic_structure", "UTF-8", "/home/hornik/tmp/scratch/RtmpPS4Uxi/file3af48f9d82b.rds")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (modelframe, modelframe_full, splines = NULL) 
{
    classes <- sapply(modelframe, class)
    classes[classes == "integer"] <- "numeric"
    multiclasses <- classes
    multiclasses[which(sapply(modelframe, function(x) length(levels(x))) > 
        2)] <- "multiclass"
    multiclasses[splines] <- "spline"
    multiclasses <- sapply(seq_along(multiclasses), function(i) {
        if (classes[i] == "factor") {
            j <- length(levels(modelframe[, i])) - 1
            baseclass <- rep(classes[i], j)
            multiclass <- rep(multiclasses[i], j)
            lev <- levels(modelframe[, i])[-1]
            ref <- levels(modelframe[, i])[1]
        }
        else {
            j <- 1
            baseclass <- rep(classes[i], j)
            multiclass <- rep(multiclasses[i], j)
            lev <- 2
            ref <- 1
        }
        cbind(baseclass, multiclass, lev, ref)
    })
    if (class(multiclasses) == "list") {
        out <- cbind(full = names(sapply(modelframe_full, class)), 
            do.call("rbind", multiclasses))
        rownames(out) <- NULL
    }
    else {
        out <- cbind(colnames(modelframe_full), t(multiclasses))
        colnames(out) <- c("full", "baseclass", "multiclass", 
            "lev", "ref")
        rownames(out) <- NULL
    }
    out <- data.frame(out, stringsAsFactors = FALSE)
    return(out)
}
<bytecode: 0x55c6808ba5c0>
<environment: namespace:themetagenomics>
 --- function search by body ---
Function create_multiclasses_table in namespace themetagenomics has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
SUMMARY: processing the following file failed:
  ‘thematic_structure.Rmd’

Error: Vignette re-building failed.
Execution halted