Error(s) in re-building vignettes:
  ...
--- re-building 'ontologySimilarity-GO-example.Rmd' using rmarkdown
--- finished re-building 'ontologySimilarity-GO-example.Rmd'

--- re-building 'ontologySimilarity-examples.Rmd' using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
ontologySimilarity
 --- call from context --- 
check_pop_sim_class(class(pop_sim), type)
 --- call from argument --- 
if (!class_name %in% names(allowed_class_type_map)) stop(paste0("Function not applicable to objects of class '", 
    class_name, "'"))
 --- R stacktrace ---
where 1: check_pop_sim_class(class(pop_sim), type)
where 2: get_sim_p.default(group = get_c_group_inds(group, rownames(pop_sim), 
    nrow(pop_sim)), pop_sim = pop_sim, type = "matrix", ...)
where 3: get_sim_p.matrix(sim_mat, group = group)
where 4: get_sim_p(sim_mat, group = group)
where 5: eval(expr, envir, enclos)
where 6: eval(expr, envir, enclos)
where 7: withVisible(eval(expr, envir, enclos))
where 8: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 9: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 12: evaluate::evaluate(...)
where 13: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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 14: 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$render, options)))
where 15: block_exec(params)
where 16: call_block(x)
where 17: process_group.block(group)
where 18: process_group(group)
where 19: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 20: process_file(text, output)
where 21: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, 
    encoding = encoding)
where 22: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    ...)
where 23: vweave_rmarkdown(...)
where 24: engine$weave(file, quiet = quiet, encoding = enc)
where 25: doTryCatch(return(expr), name, parentenv, handler)
where 26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 27: tryCatchList(expr, classes, parentenv, handlers)
where 28: tryCatch({
    engine$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 29: tools:::.buildOneVignette("ontologySimilarity-examples.Rmd", 
    "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ontologySimilarity.Rcheck/vign_test/ontologySimilarity", 
    TRUE, FALSE, "ontologySimilarity-examples", "", "/tmp/RtmpkhLgku/file6292daa69d4.rds")

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (class_name, type) 
{
    if (!class_name %in% names(allowed_class_type_map)) 
        stop(paste0("Function not applicable to objects of class '", 
            class_name, "'"))
    if (!(allowed_class_type_map[class_name] == type)) 
        stop(paste0("Class-type mismatch"))
}
<bytecode: 0x535caf8>
<environment: namespace:ontologySimilarity>
 --- function search by body ---
Function check_pop_sim_class in namespace ontologySimilarity has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
--- re-building 'ontologySimilarity-introduction.Rmd' using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
ontologySimilarity
 --- call from context --- 
check_pop_sim_class(class(pop_sim), type)
 --- call from argument --- 
if (!class_name %in% names(allowed_class_type_map)) stop(paste0("Function not applicable to objects of class '", 
    class_name, "'"))
 --- R stacktrace ---
where 1: check_pop_sim_class(class(pop_sim), type)
where 2: get_sim.default(group = get_c_group_inds(group, rownames(pop_sim), 
    nrow(pop_sim)), pop_sim = pop_sim, type = "matrix", ...)
where 3: get_sim.matrix(sim_mat, group = 1:3)
where 4: get_sim(sim_mat, group = 1:3)
where 5: eval(expr, envir, enclos)
where 6: eval(expr, envir, enclos)
where 7: withVisible(eval(expr, envir, enclos))
where 8: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 9: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 12: evaluate::evaluate(...)
where 13: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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 14: 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$render, options)))
where 15: block_exec(params)
where 16: call_block(x)
where 17: process_group.block(group)
where 18: process_group(group)
where 19: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 20: process_file(text, output)
where 21: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, 
    encoding = encoding)
where 22: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    ...)
where 23: vweave_rmarkdown(...)
where 24: engine$weave(file, quiet = quiet, encoding = enc)
where 25: doTryCatch(return(expr), name, parentenv, handler)
where 26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 27: tryCatchList(expr, classes, parentenv, handlers)
where 28: tryCatch({
    engine$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 29: tools:::.buildOneVignette("ontologySimilarity-introduction.Rmd", 
    "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ontologySimilarity.Rcheck/vign_test/ontologySimilarity", 
    TRUE, FALSE, "ontologySimilarity-introduction", "", "/tmp/RtmpkhLgku/file629215a61566.rds")

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (class_name, type) 
{
    if (!class_name %in% names(allowed_class_type_map)) 
        stop(paste0("Function not applicable to objects of class '", 
            class_name, "'"))
    if (!(allowed_class_type_map[class_name] == type)) 
        stop(paste0("Class-type mismatch"))
}
<bytecode: 0x6559da8>
<environment: namespace:ontologySimilarity>
 --- function search by body ---
Function check_pop_sim_class in namespace ontologySimilarity has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
SUMMARY: processing the following files failed:
  'ontologySimilarity-examples.Rmd'
  'ontologySimilarity-introduction.Rmd'

Error: Vignette re-building failed.
Execution halted