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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: 37797 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/RtmpRjyT6y/xshell8fad342e84e1' 2>&1
 ERROR
--- re-building ‘TCGAWorkflow.Rmd’ using rmarkdown
2024-11-15 13:14:05.690 R[37797:420965893] XType: com.apple.fonts is not accessible.
2024-11-15 13:14:05.690 R[37797:420965893] XType: XTFontStaticRegistry is enabled.

 *** caught segfault ***
address 0xfffffffd1235c1c0, cause 'memory not mapped'

Traceback:
 1: GADEM(sequence, verbose = FALSE, genome = Hsapiens)
 2: eval(expr, envir)
 3: eval(expr, envir)
 4: withVisible(eval(expr, envir))
 5: withCallingHandlers(code, message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = invokeRestart("eval_error",             cnd))})
 6: eval(call)
 7: eval(call)
 8: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
 9: doWithOneRestart(return(expr), restart)
10: withOneRestart(expr, restarts[[1L]])
11: withRestartList(expr, restarts[-nr])
12: doWithOneRestart(return(expr), restart)
13: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
14: withRestartList(expr, restarts[-nr])
15: doWithOneRestart(return(expr), restart)
16: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
17: withRestartList(expr, restarts)
18: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE,     eval_error = function(cnd) {        signalCondition(cnd)        stop(cnd)    })
19: evaluate::evaluate(...)
20: 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$render, options))
21: in_dir(input_dir(), expr)
22: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
23: eng_r(options)
24: block_exec(params)
25: call_block(x)
26: process_group(group)
27: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
28: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
29: process_file(text, output)
30: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
31: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
32: vweave_rmarkdown(...)
33: engine$weave(file, quiet = quiet, encoding = enc)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: tryCatch({    engine$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)))})
38: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...