* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/causalCmprsk.Rcheck’
* using R Under development (unstable) (2022-04-03 r82074)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘causalCmprsk/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘causalCmprsk’ version ‘1.0.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘causalCmprsk’ can be installed ... [15s/25s] OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [27s/36s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [14s/19s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘cmp_rsk_RHC.Rmd’ using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
kableExtra
 --- call from context --- 
fun(libname, pkgname)
 --- call from argument --- 
!is.null(rmarkdown::metadata$output) && rmarkdown::metadata$output %in% 
    c("ioslides_presentation", "slidy_presentation", "gitbook", 
        "bookdown::gitbook", "radix_article", "radix::radix_article", 
        "distill_article", "distill::distill_article")
 --- R stacktrace ---
where 1: fun(libname, pkgname)
where 2: doTryCatch(return(expr), name, parentenv, handler)
where 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 4: tryCatchList(expr, classes, parentenv, handlers)
where 5: tryCatch(fun(libname, pkgname), error = identity)
where 6: runHook(".onLoad", env, package.lib, package)
where 7: loadNamespace(package, ...)
where 8: doTryCatch(return(expr), name, parentenv, handler)
where 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 10: tryCatchList(expr, classes, parentenv, handlers)
where 11: tryCatch(loadNamespace(package, ...), error = function(e) e)
where 12: requireNamespace(package, quietly = TRUE)
where 13: eval(expr, envir, enclos)
where 14: eval(expr, envir, enclos)
where 15: eval_with_user_handlers(expr, envir, enclos, user_handlers)
where 16: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
where 17: withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)
where 18: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler))
where 19: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)))
where 20: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 21: evaluate::evaluate(...)
where 22: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), 
    keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else {
        if (options$error && options$include) 
            0L
        else 2L
    }, output_handler = knit_handlers(options$render, options))
where 23: in_dir(input_dir(), expr)
where 24: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 
    stop_on_error = if (is.numeric(options$error)) options$error else {
        if (options$error && options$include) 
            0L
        else 2L
    }, output_handler = knit_handlers(options$render, options)))
where 25: eng_r(options)
where 26: block_exec(params)
where 27: call_block(x)
where 28: process_group.block(group)
where 29: process_group(group)
where 30: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 31: process_file(text, output)
where 32: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 33: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    output_dir = getwd(), ...)
where 34: vweave_rmarkdown(...)
where 35: engine$weave(file, quiet = quiet, encoding = enc)
where 36: doTryCatch(return(expr), name, parentenv, handler)
where 37: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 38: tryCatchList(expr, classes, parentenv, handlers)
where 39: tryCatch({
    engine$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)
    }
    outputs <- c(outputs, output)
}, error = function(e) {
    thisOK <<- FALSE
    fails <<- c(fails, file)
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 40: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-LENGTH1/causalCmprsk.Rcheck/vign_test/causalCmprsk")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (libname = find.package("kableExtra"), pkgname = "kableExtra") 
{
    if (knitr::is_latex_output()) {
        load_packages <- getOption("kableExtra.latex.load_packages", 
            default = TRUE)
        if (load_packages) {
            usepackage_latex("booktabs")
            usepackage_latex("longtable")
            usepackage_latex("array")
            usepackage_latex("multirow")
            usepackage_latex("wrapfig")
            usepackage_latex("float")
            usepackage_latex("colortbl")
            usepackage_latex("pdflscape")
            usepackage_latex("tabu")
            usepackage_latex("threeparttable")
            usepackage_latex("threeparttablex")
            usepackage_latex("ulem", "normalem")
            usepackage_latex("makecell")
            usepackage_latex("xcolor")
        }
    }
    auto_format <- getOption("kableExtra.auto_format", default = TRUE)
    if (auto_format) 
        auto_set_format()
    if (!is.null(rmarkdown::metadata$output) && rmarkdown::metadata$output %in% 
        c("ioslides_presentation", "slidy_presentation", "gitbook", 
            "bookdown::gitbook", "radix_article", "radix::radix_article", 
            "distill_article", "distill::distill_article")) {
        options(kableExtra.html.bsTable = TRUE)
    }
    if (!is.null(knitr::opts_knit$get("rmarkdown.pandoc.to")) && 
        knitr::opts_knit$get("rmarkdown.pandoc.to") %in% c("epub3", 
            "epub")) {
        options(kableExtra.knit_print.dependency = FALSE)
    }
}
<bytecode: 0xf0f1ce0>
<environment: namespace:kableExtra>
 --- function search by body ---
Function .onLoad in namespace kableExtra has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical

* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/causalCmprsk.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:13.07, 122.92 + 12.26