Open zchenmr opened 1 month ago
Rmonize v1.1.0.9000, madshapR v1.1.0.9002
I get different errors when I run harmonized_dossier_visualize with or without an harmonized_dossier_summary input argument.
harmonized_dossier_visualize
With the input:
harmonized_dossier_visualize(harmonized_dossier = harmonized_dossier, harmonized_dossier_summary = harmonized_dossier_summary, bookdown_path = "path")
Error:
Traceback:
46: stop(fallback) 45: signal_abort(cnd) 44: cnd_signal(cnd) 43: (function (cnd) { cnd$subscript_action <- subscript_action(type) cnd$subscript_elt <- "column" cnd_signal(cnd) })(structure(list(message = "", trace = structure(list(call = list( variable_visualize(dataset, col = "adm_id_participant", data_dict = data_dict, group_by = "Rmonize::harmonized_col_dataset", valueType_guess = "FALSE", variable_summary = dataset_summary), unique(pull(`Variables summary (all)` %>% dplyr::filter(.data$name %in% col) %>% select(starts_with("Grouping variable:")))), pull(`Variables summary (all)` %>% dplyr::filter(.data$name %in% col) %>% select(starts_with("Grouping variable:"))), pull.data.frame(`Variables summary (all)` %>% dplyr::filter(.data$name %in% col) %>% select(starts_with("Grouping variable:"))), tidyselect::vars_pull(names(.data), !!enquo(var)), pull_as_location2(loc, n, vars, error_arg = error_arg, error_call = error_call), with_subscript_errors(type = "pull", { i <- vctrs::vec_as_subscript2(i, logical = "error", arg = error_arg, call = error_call) if (length(i) != 1) { ... 42: signalCondition(cnd) 41: signal_abort(cnd) 40: cnd_signal(x$err) 39: result_get(vec_as_location2_result(i, n = n, names = NULL, negative = negative, missing = missing, arg = arg, call = call)) 38: vctrs::num_as_location2(i, n = n, negative = "ignore", arg = error_arg, call = error_call) 37: withCallingHandlers(expr, vctrs_error_subscript = function(cnd) { cnd$subscript_action <- subscript_action(type) cnd$subscript_elt <- "column" cnd_signal(cnd) }) 36: with_subscript_errors(type = "pull", { i <- vctrs::vec_as_subscript2(i, logical = "error", arg = error_arg, call = error_call) if (length(i) != 1) { cli::cli_abort("{.arg {error_arg}} must select exactly one column.", call = error_call) } if (is.numeric(i)) { vctrs::num_as_location2(i, n = n, negative = "ignore", arg = error_arg, call = error_call) } else { vctrs::vec_as_location2(i, n = n, names = names, arg = error_arg, call = error_call, ) } }) 35: pull_as_location2(loc, n, vars, error_arg = error_arg, error_call = error_call) 34: tidyselect::vars_pull(names(.data), !!enquo(var)) 33: pull.data.frame(`Variables summary (all)` %>% dplyr::filter(.data$name %in% col) %>% select(starts_with("Grouping variable:"))) 32: pull(`Variables summary (all)` %>% dplyr::filter(.data$name %in% col) %>% select(starts_with("Grouping variable:"))) 31: unique(pull(`Variables summary (all)` %>% dplyr::filter(.data$name %in% col) %>% select(starts_with("Grouping variable:")))) 30: variable_visualize(dataset, col = "adm_id_participant", data_dict = data_dict, group_by = "Rmonize::harmonized_col_dataset", valueType_guess = "FALSE", variable_summary = dataset_summary) 29: eval(expr, envir, enclos) 28: eval(expr, envir, enclos) 27: eval_with_user_handlers(expr, envir, enclos, user_handlers) 26: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)) 25: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler) 24: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)) 23: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))) 22: evaluate_call(expr, parsed$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) 21: 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$render, options)) 19: in_dir(input_dir(), expr) 18: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))) 17: eng_r(options) 16: block_exec(params) 15: call_block(x) 14: process_group(group) 13: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)) 12: 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(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 11: process_file(text, output) 10: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 9: rmarkdown::render(main, output_format, ..., clean = clean, envir = envir) 8: render_cur_session(files, main, config, output_format, clean, envir, ...) 7: render_book(input = paste0("index.Rmd")) 6: in_dir(dir = bookdown_path, expr = render_book(input = paste0("index.Rmd"))) 5: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage")) 4: suppressMessages({ in_dir(dir = bookdown_path, expr = render_book(input = paste0("index.Rmd"))) }) 3: bookdown_render(path_to, overwrite = FALSE) 2: dataset_visualize(dataset = pooled_harmonized_dataset, group_by = attributes(pooled_harmonized_dataset)$`Rmonize::harmonized_col_dataset`, bookdown_path = bookdown_path, taxonomy = taxonomy, valueType_guess = valueType_guess, dataset_summary = harmonized_dossier_summary) 1: harmonized_dossier_visualize(harmonized_dossier = harmonized_anderson_t1_qx, harmonized_dossier_summary = stat_report_anderson_t1_qx, bookdown_path = "commons/reports/post_harmo/SaskCov_t1_qx_visual_report_3_2")
Without the input:
harmonized_dossier_visualize(harmonized_dossier = harmonized_dossier, bookdown_path = "path")
21: stop(fallback) 20: signal_abort(cnd, .file) 19: abort(message, class = error_class, parent = parent, call = error_call) 18: h(simpleError(msg, call)) 17: .handleSimpleError(function (cnd) { local_error_context(dots, i = frame[[i_sym]], mask = mask) if (inherits(cnd, "dplyr:::internal_error")) { parent <- error_cnd(message = bullets(cnd)) } else { parent <- cnd } message <- c(cnd_bullet_header(action), i = if (has_active_group_context(mask)) cnd_bullet_cur_group_label()) abort(message, class = error_class, parent = parent, call = error_call) }, "object 'label:en' not found", base::quote(NULL)) 16: ifelse(.data$name == "-190719831562453", "-190719831562453", `label:en`) 15: .Call(dplyr_mask_eval_all_mutate, quo, private) 14: eval() 13: mask$eval_all_mutate(quo) 12: mutate_col(dots[[i]], data, mask, new_columns) 11: withCallingHandlers(for (i in seq_along(dots)) { poke_error_context(dots, i, mask = mask) context_poke("column", old_current_column) new_columns <- mutate_col(dots[[i]], data, mask, new_columns) }, error = dplyr_error_handler(dots = dots, mask = mask, bullets = mutate_bullets, error_call = error_call, error_class = "dplyr:::mutate_error"), warning = dplyr_warning_handler(state = warnings_state, mask = mask, error_call = error_call)) 10: mutate_cols(.data, dplyr_quosures(...), by) 9: mutate.data.frame(., missing = ifelse(.data$name == "-190719831562453", TRUE, .data$missing), `:=`(!!as_any_symbol(label), ifelse(.data$name == "-190719831562453", "-190719831562453", !!as_any_symbol(label)))) 8: mutate(., missing = ifelse(.data$name == "-190719831562453", TRUE, .data$missing), `:=`(!!as_any_symbol(label), ifelse(.data$name == "-190719831562453", "-190719831562453", !!as_any_symbol(label)))) 7: data_dict_group_by$Categories %>% mutate(missing = ifelse(.data$name == "-190719831562453", TRUE, .data$missing), `:=`(!!as_any_symbol(label), ifelse(.data$name == "-190719831562453", "-190719831562453", !!as_any_symbol(label)))) 6: list2(...) 5: bind_rows(data_dict[["Categories"]], data_dict_group_by$Categories %>% mutate(missing = ifelse(.data$name == "-190719831562453", TRUE, .data$missing), `:=`(!!as_any_symbol(label), ifelse(.data$name == "-190719831562453", "-190719831562453", !!as_any_symbol(label))))) 4: distinct(.) 3: bind_rows(data_dict[["Categories"]], data_dict_group_by$Categories %>% mutate(missing = ifelse(.data$name == "-190719831562453", TRUE, .data$missing), `:=`(!!as_any_symbol(label), ifelse(.data$name == "-190719831562453", "-190719831562453", !!as_any_symbol(label))))) %>% distinct() 2: dataset_summarize(dataset = pooled_harmonized_dataset, group_by = attributes(pooled_harmonized_dataset)$`Rmonize::harmonized_col_dataset`, taxonomy = taxonomy, valueType_guess = valueType_guess) 1: harmonized_dossier_visualize(harmonized_dossier = harmonized_anderson_t1_qx, bookdown_path = "commons/reports/post_harmo/SaskCov_t1_qx_visual_report_3_2")
Rmonize v1.1.0.9000, madshapR v1.1.0.9002
I get different errors when I run
harmonized_dossier_visualizewith or without an harmonized_dossier_summary input argument.With the input:
Error:
Traceback:
Without the input:
Error:
Traceback: