bensoltoff
commented
3 years ago What happens if you run the code interactively in RStudio? Does it all run? Looks like the issue is when you load one of the data files. It should be near the top of your document.
On Sun, Jan 31, 2021, 6:19 PM akerah notifications@github.com wrote:
Tried to knit and I got this long scary notice
caught segfault address 0x68, cause 'memory not mapped'
Traceback: 1: readtokens(data, tokenizer, col_specs, colnames, locale, n_max, progress) 2: readtokens(ds, tokenizer, spec$cols, names(spec$cols), locale = locale, n_max = n_max, progress = progress) 3: read_delimited(file, tokenizer, col_names = col_names, col_types = col_types, locale = locale, skip = skip, skip_empty_rows = skip_empty_rows, comment = comment, n_max = n_max, guess_max = guess_max, progress = progress) 4: read_csv("data/scdb-case.csv") 5: eval(expr, envir, enclos) 6: eval(expr, envir, enclos) 7: withVisible(eval(expr, envir, enclos)) 8: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler) 9: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)) 10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))) 11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing) 12: evaluate::evaluate(...) 13: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)) 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$render, options))) 15: block_exec(params) 16: call_block(x) 17: process_group.block(group) 18: process_group(group) 19: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") }) 20: process_file(text, output) 21: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 22: rmarkdown::render("/home/akerah/Mackey_github/hw03/scotus.Rmd", encoding = "UTF-8", knit_root_dir = "~/Mackey_github/hw03") An irrecoverable exception occurred. R is aborting now ...
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akerah
Tried to knit and I got this long scary notice
caught segfault address 0x68, cause 'memory not mapped'
Traceback: 1: readtokens(data, tokenizer, col_specs, colnames, locale, n_max, progress) 2: readtokens(ds, tokenizer, spec$cols, names(spec$cols), locale = locale, n_max = n_max, progress = progress) 3: read_delimited(file, tokenizer, col_names = col_names, col_types = col_types, locale = locale, skip = skip, skip_empty_rows = skip_empty_rows, comment = comment, n_max = n_max, guess_max = guess_max, progress = progress) 4: read_csv("data/scdb-case.csv") 5: eval(expr, envir, enclos) 6: eval(expr, envir, enclos) 7: withVisible(eval(expr, envir, enclos)) 8: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler) 9: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)) 10: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))) 11: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing) 12: evaluate::evaluate(...) 13: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)) 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$render, options))) 15: block_exec(params) 16: call_block(x) 17: process_group.block(group) 18: process_group(group) 19: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") }) 20: process_file(text, output) 21: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 22: rmarkdown::render("/home/akerah/Mackey_github/hw03/scotus.Rmd", encoding = "UTF-8", knit_root_dir = "~/Mackey_github/hw03") An irrecoverable exception occurred. R is aborting now ...