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R CMD BUILD
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* checking for file ‘CBN2Path/DESCRIPTION’ ... OK
* preparing ‘CBN2Path’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘CBN2Path.Rmd’ using rmarkdown
*** caught segfault ***
address 0xc0, cause 'memory not mapped'
Traceback:
1: hcbnSingle(datasets, anneal, temp, annealing_steps, epsilon)
2: hcbn(bc)
3: pathProbQuartetHCBN(g_mat2)
4: eval(expr, envir)
5: eval(expr, envir)
6: withVisible(eval(expr, envir))
7: 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 = NULL)})
8: eval(call)
9: eval(call)
10: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
11: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
13: withRestartList(expr, restarts[-nr])
14: doWithOneRestart(return(expr), restart)
15: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
16: withRestartList(expr, restarts)
17: withRestarts(with_handlers({ for (expr in tle$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)
18: evaluate::evaluate(...)
19: 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$render, options))
20: in_dir(input_dir(), expr)
21: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
22: eng_r(options)
23: block_exec(params)
24: call_block(x)
25: process_group(group)
26: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } })
27: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (xfun::pkg_available("rlang", "1.0.0")) { if (is_R_CMD_build() || is_R_CMD_check()) { cnd = tryCatch(rlang::entrace(e), error = identity) error <<- format(cnd) } else { rlang::entrace(e) } } }), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
28: process_file(text, output)
29: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
30: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
31: vweave_rmarkdown(...)
32: engine$weave(file, quiet = quiet, encoding = enc)
33: doTryCatch(return(expr), name, parentenv, handler)
34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch({ engine$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)))})
37: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
sh: error while loading shared libraries: libc.so.6: cannot open shared object file: Error 24
Segmentation fault (core dumped)