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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAWorkflow
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* checking for file ‘TCGAWorkflow/DESCRIPTION’ ... OK
* preparing ‘TCGAWorkflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 40060 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpNnnrNg/xshell98c12b9ff4b0' 2>&1
 ERROR
--- re-building ‘TCGAWorkflow.Rmd’ using rmarkdown
2023-09-22 11:12:48.322 R[40060:1332693704] XType: com.apple.fonts is not accessible.
2023-09-22 11:12:48.323 R[40060:1332693704] XType: XTFontStaticRegistry is enabled.

 *** caught segfault ***
address 0xfffffffd179711c0, cause 'memory not mapped'

Traceback:
 1: GADEM(sequence, verbose = FALSE, genome = Hsapiens)
 2: eval(expr, envir, enclos)
 3: eval(expr, envir, enclos)
 4: eval_with_user_handlers(expr, envir, enclos, user_handlers)
 5: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
 6: withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)
 7: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler))
 8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)))
 9: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,     include_timing = include_timing)
10: evaluate::evaluate(...)
11: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else 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))
12: in_dir(input_dir(), expr)
13: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$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$render, options)))
14: eng_r(options)
15: block_exec(params)
16: call_block(x)
17: process_group.block(group)
18: process_group(group)
19: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
20: withCallingHandlers(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     error = function(e) {        setwd(wd)        write_utf8(res, output %n% stdout())        message("\nQuitting from lines ", paste(current_lines(i),             collapse = "-"), if (labels[i] != "")             sprintf(" [%s]", labels[i]), sprintf(" (%s)", knit_concord$get("infile")))    })
21: process_file(text, output)
22: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
23: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
24: vweave_rmarkdown(...)
25: engine$weave(file, quiet = quiet, encoding = enc)
26: doTryCatch(return(expr), name, parentenv, handler)
27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
28: tryCatchList(expr, classes, parentenv, handlers)
29: tryCatch({    engine$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)    }    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)))})
30: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...