Last updated on 2026-07-17 09:51:14 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.1 | 14.93 | 334.43 | 349.36 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.1 | 11.94 | 133.95 | 145.89 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.1 | 24.00 | 339.96 | 363.96 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.1 | 11.00 | 227.45 | 238.45 | OK | |
| r-devel-windows-x86_64 | 1.1.1 | 17.00 | 316.00 | 333.00 | OK | |
| r-patched-linux-x86_64 | 1.1.1 | 16.22 | 319.08 | 335.30 | OK | |
| r-release-linux-x86_64 | 1.1.1 | 14.39 | 317.44 | 331.83 | OK | |
| r-release-macos-arm64 | 1.1.1 | 4.00 | 74.00 | 78.00 | OK | |
| r-release-macos-x86_64 | 1.1.1 | 10.00 | 319.00 | 329.00 | OK | |
| r-release-windows-x86_64 | 1.1.1 | 16.00 | 304.00 | 320.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.1 | OK | ||||
| r-oldrel-macos-x86_64 | 1.1.1 | 9.00 | 319.00 | 328.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.1 | 23.00 | 430.00 | 453.00 | OK |
Version: 1.1.1
Check: examples
Result: ERROR
Running examples in ‘whomds-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: table_weightedpct
> ### Title: Calculate table of percentages or N of response distribution for
> ### survey items, survey weighted, disaggregated
> ### Aliases: table_weightedpct
>
> ### ** Examples
>
> table_weightedpct(df_adults,
+ vars_ids = c("HHID", "PSU"),
+ vars_strata = "strata",
+ vars_weights = "weight",
+ formula_vars = paste0("EF",1:10),
+ formula_vars_levels = 1:5,
+ by_vars = "sex")
Warning in table_weightedpct(df_adults, vars_ids = c("HHID", "PSU"), vars_strata = "strata", :
You may have issues with lonely PSUs if you have not set: options(survey.lonely.psu = "adjust")
*** caught segfault ***
address 0x76, cause 'memory not mapped'
Traceback:
1: .Call(dplyr_mask_eval_all_summarise, quo, private)
2: eval()
3: mask$eval_all_summarise(quo)
4: FUN(X[[i]], ...)
5: lapply(.x, .f, ...)
6: map(quosures, summarise_eval_one, mask = mask)
7: withCallingHandlers({ for (i in seq_along(dots)) { poke_error_context(dots, i, mask = mask) context_poke("column", old_current_column) dot <- dots[[i]] dot <- expand_pick(dot, mask) quosures <- expand_across(dot) quosures_results <- map(quosures, summarise_eval_one, mask = mask) for (k in seq_along(quosures)) { quo <- quosures[[k]] quo_data <- attr(quo, "dplyr:::data") quo_result <- quosures_results[[k]] if (is.null(quo_result)) { next } types_k <- quo_result$types chunks_k <- quo_result$chunks results_k <- quo_result$results if (!quo_data$is_named && is.data.frame(types_k)) { chunks_extracted <- .Call(dplyr_extract_chunks, chunks_k, types_k) types_k_names <- names(types_k) for (j in seq_along(chunks_extracted)) { mask$add_one(name = types_k_names[j], chunks = chunks_extracted[[j]], result = results_k[[j]]) } chunks <- append(chunks, chunks_extracted) types <- append(types, as.list(types_k)) results <- append(results, results_k) out_names <- c(out_names, types_k_names) } else { name <- dplyr_quosure_name(quo_data) mask$add_one(name = name, chunks = chunks_k, result = results_k) chunks <- append(chunks, list(chunks_k)) types <- append(types, list(types_k)) results <- append(results, list(results_k)) out_names <- c(out_names, name) } } } if (verb == "summarise") { .Call(dplyr_summarise_check_all_size_one, chunks, n_groups) group_sizes <- NULL } else { group_sizes <- .Call(dplyr_reframe_recycle_horizontally_in_place, chunks, results, n_groups) for (i in seq_along(chunks)) { if (is.null(results[[i]])) { results[[i]] <- vec_c(!!!chunks[[i]], .ptype = types[[i]]) } } }}, error = function(cnd) { if (inherits(cnd, "dplyr:::reframe_incompatible_size")) { action <- "recycle" i <- cnd$dplyr_error_data$index_expression } else if (inherits(cnd, "dplyr:::summarise_incompatible_size")) { action <- "compute" i <- cnd$dplyr_error_data$index_expression } else { action <- "compute" i <- i } handler <- dplyr_error_handler(dots = dots, mask = mask, bullets = summarise_bullets, error_call = error_call, action = action) handler(cnd)}, warning = dplyr_warning_handler(state = warnings_state, mask = mask, error_call = error_call))
8: summarise_cols(.data, dplyr_quosures(...), by, "summarise")
9: summarise.grouped_df(.data$variables, !!!.dots, .groups = .groups)
10: dplyr::summarise(.data$variables, !!!.dots, .groups = .groups)
11: summarise.grouped_svy(., prop = survey_mean(na.rm = TRUE))
12: summarize(., prop = survey_mean(na.rm = TRUE))
13: mutate(., prop = prop * 100)
14: des %>% group_by_at(c(by_vars, "item", "resp")) %>% summarize(prop = survey_mean(na.rm = TRUE)) %>% mutate(prop = prop * 100)
15: table_weightedpct(df_adults, vars_ids = c("HHID", "PSU"), vars_strata = "strata", vars_weights = "weight", formula_vars = paste0("EF", 1:10), formula_vars_levels = 1:5, by_vars = "sex")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(whomds)
Loading required package: psych
Attaching package: 'psych'
The following object is masked from 'package:testthat':
describe
Thank you for using whomds. To learn more about the WHO Model Disability Survey (MDS) and for contact information, go to https://www.who.int/health-topics/disability
>
> test_check("whomds")
*** caught segfault ***
address 0xe600000113, cause 'memory not mapped'
Traceback:
1: .Call(dplyr_mask_eval_all_summarise, quo, private)
2: eval()
3: mask$eval_all_summarise(quo)
4: FUN(X[[i]], ...)
5: lapply(.x, .f, ...)
6: map(quosures, summarise_eval_one, mask = mask)
7: withCallingHandlers({ for (i in seq_along(dots)) { poke_error_context(dots, i, mask = mask) context_poke("column", old_current_column) dot <- dots[[i]] dot <- expand_pick(dot, mask) quosures <- expand_across(dot) quosures_results <- map(quosures, summarise_eval_one, mask = mask) for (k in seq_along(quosures)) { quo <- quosures[[k]] quo_data <- attr(quo, "dplyr:::data") quo_result <- quosures_results[[k]] if (is.null(quo_result)) { next } types_k <- quo_result$types chunks_k <- quo_result$chunks results_k <- quo_result$results if (!quo_data$is_named && is.data.frame(types_k)) { chunks_extracted <- .Call(dplyr_extract_chunks, chunks_k, types_k) types_k_names <- names(types_k) for (j in seq_along(chunks_extracted)) { mask$add_one(name = types_k_names[j], chunks = chunks_extracted[[j]], result = results_k[[j]]) } chunks <- append(chunks, chunks_extracted) types <- append(types, as.list(types_k)) results <- append(results, results_k) out_names <- c(out_names, types_k_names) } else { name <- dplyr_quosure_name(quo_data) mask$add_one(name = name, chunks = chunks_k, result = results_k) chunks <- append(chunks, list(chunks_k)) types <- append(types, list(types_k)) results <- append(results, list(results_k)) out_names <- c(out_names, name) } } } if (verb == "summarise") { .Call(dplyr_summarise_check_all_size_one, chunks, n_groups) group_sizes <- NULL } else { group_sizes <- .Call(dplyr_reframe_recycle_horizontally_in_place, chunks, results, n_groups) for (i in seq_along(chunks)) { if (is.null(results[[i]])) { results[[i]] <- vec_c(!!!chunks[[i]], .ptype = types[[i]]) } } }}, error = function(cnd) { if (inherits(cnd, "dplyr:::reframe_incompatible_size")) { action <- "recycle" i <- cnd$dplyr_error_data$index_expression } else if (inherits(cnd, "dplyr:::summarise_incompatible_size")) { action <- "compute" i <- cnd$dplyr_error_data$index_expression } else { action <- "compute" i <- i } handler <- dplyr_error_handler(dots = dots, mask = mask, bullets = summarise_bullets, error_call = error_call, action = action) handler(cnd)}, warning = dplyr_warning_handler(state = warnings_state, mask = mask, error_call = error_call))
8: summarise_cols(.data, dplyr_quosures(...), by, "summarise")
9: summarise.grouped_df(.data$variables, !!!.dots, .groups = .groups)
10: dplyr::summarise(.data$variables, !!!.dots, .groups = .groups)
11: summarise.grouped_svy(., prop = survey_mean(na.rm = TRUE))
12: summarize(., prop = survey_mean(na.rm = TRUE))
13: mutate(., prop = prop * 100)
14: des %>% group_by_at(c(by_vars, "item", "resp")) %>% summarize(prop = survey_mean(na.rm = TRUE)) %>% mutate(prop = prop * 100)
15: table_weightedpct(df_adults, vars_ids = c("PSU", "HHID"), vars_strata = "strata", vars_weights = "weight", formula_vars = formula_vars, formula_vars_levels = formula_vars_levels, by_vars = by_vars)
16: eval(code, test_env)
17: eval(code, test_env)
18: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
23: doWithOneRestart(return(expr), restart)
24: withOneRestart(expr, restarts[[1L]])
25: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
26: test_code(code, parent.frame())
27: test_that("Dimensions as multiple of formula_vars, levels, and by_vars", { formula_vars <- paste0("EF", 1:10) formula_vars_levels <- 1:5 by_vars <- "sex" tab <- table_weightedpct(df_adults, vars_ids = c("PSU", "HHID"), vars_strata = "strata", vars_weights = "weight", formula_vars = formula_vars, formula_vars_levels = formula_vars_levels, by_vars = by_vars) expect_equal(nrow(tab), length(formula_vars) * length(formula_vars_levels) * length(levels(dplyr::pull(df_adults, by_vars)))) expect_equal(ncol(tab), 4) })
28: eval(code, test_env)
29: eval(code, test_env)
30: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
35: doWithOneRestart(return(expr), restart)
36: withOneRestart(expr, restarts[[1L]])
37: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
38: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
39: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
40: FUN(X[[i]], ...)
41: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
42: doTryCatch(return(expr), name, parentenv, handler)
43: tryCatchOne(expr, names, parentenv, handlers[[1L]])
44: tryCatchList(expr, classes, parentenv, handlers)
45: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
46: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
47: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
48: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
49: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
50: test_check("whomds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘c1_background_EN.Rmd’ using rmarkdown
--- finished re-building ‘c1_background_EN.Rmd’
--- re-building ‘c1_background_ES.Rmd’ using rmarkdown
--- finished re-building ‘c1_background_ES.Rmd’
--- re-building ‘c2_getting_started_EN.Rmd’ using rmarkdown
--- finished re-building ‘c2_getting_started_EN.Rmd’
--- re-building ‘c2_getting_started_ES.Rmd’ using rmarkdown
--- finished re-building ‘c2_getting_started_ES.Rmd’
--- re-building ‘c3_rasch_adults_EN.Rmd’ using rmarkdown
--- finished re-building ‘c3_rasch_adults_EN.Rmd’
--- re-building ‘c3_rasch_adults_ES.Rmd’ using rmarkdown
--- finished re-building ‘c3_rasch_adults_ES.Rmd’
--- re-building ‘c4_rasch_children_EN.Rmd’ using rmarkdown
--- finished re-building ‘c4_rasch_children_EN.Rmd’
--- re-building ‘c4_rasch_children_ES.Rmd’ using rmarkdown
--- finished re-building ‘c4_rasch_children_ES.Rmd’
--- re-building ‘c5_best_practices_EN.Rmd’ using rmarkdown
--- finished re-building ‘c5_best_practices_EN.Rmd’
--- re-building ‘c5_best_practices_ES.Rmd’ using rmarkdown
--- finished re-building ‘c5_best_practices_ES.Rmd’
--- re-building ‘c6_after_rasch_EN.Rmd’ using rmarkdown
*** caught segfault ***
address 0x400000003, cause 'memory not mapped'
Traceback:
1: .Call(dplyr_mask_eval_all_summarise, quo, private)
2: eval()
3: mask$eval_all_summarise(quo)
4: FUN(X[[i]], ...)
5: lapply(.x, .f, ...)
6: map(quosures, summarise_eval_one, mask = mask)
7: withCallingHandlers({ for (i in seq_along(dots)) { poke_error_context(dots, i, mask = mask) context_poke("column", old_current_column) dot <- dots[[i]] dot <- expand_pick(dot, mask) quosures <- expand_across(dot) quosures_results <- map(quosures, summarise_eval_one, mask = mask) for (k in seq_along(quosures)) { quo <- quosures[[k]] quo_data <- attr(quo, "dplyr:::data") quo_result <- quosures_results[[k]] if (is.null(quo_result)) { next } types_k <- quo_result$types chunks_k <- quo_result$chunks results_k <- quo_result$results if (!quo_data$is_named && is.data.frame(types_k)) { chunks_extracted <- .Call(dplyr_extract_chunks, chunks_k, types_k) types_k_names <- names(types_k) for (j in seq_along(chunks_extracted)) { mask$add_one(name = types_k_names[j], chunks = chunks_extracted[[j]], result = results_k[[j]]) } chunks <- append(chunks, chunks_extracted) types <- append(types, as.list(types_k)) results <- append(results, results_k) out_names <- c(out_names, types_k_names) } else { name <- dplyr_quosure_name(quo_data) mask$add_one(name = name, chunks = chunks_k, result = results_k) chunks <- append(chunks, list(chunks_k)) types <- append(types, list(types_k)) results <- append(results, list(results_k)) out_names <- c(out_names, name) } } } if (verb == "summarise") { .Call(dplyr_summarise_check_all_size_one, chunks, n_groups) group_sizes <- NULL } else { group_sizes <- .Call(dplyr_reframe_recycle_horizontally_in_place, chunks, results, n_groups) for (i in seq_along(chunks)) { if (is.null(results[[i]])) { results[[i]] <- vec_c(!!!chunks[[i]], .ptype = types[[i]]) } } }}, error = function(cnd) { if (inherits(cnd, "dplyr:::reframe_incompatible_size")) { action <- "recycle" i <- cnd$dplyr_error_data$index_expression } else if (inherits(cnd, "dplyr:::summarise_incompatible_size")) { action <- "compute" i <- cnd$dplyr_error_data$index_expression } else { action <- "compute" i <- i } handler <- dplyr_error_handler(dots = dots, mask = mask, bullets = summarise_bullets, error_call = error_call, action = action) handler(cnd)}, warning = dplyr_warning_handler(state = warnings_state, mask = mask, error_call = error_call))
8: summarise_cols(.data, dplyr_quosures(...), by, "summarise")
9: summarise.grouped_df(.data$variables, !!!.dots, .groups = .groups)
10: dplyr::summarise(.data$variables, !!!.dots, .groups = .groups)
11: summarise.grouped_svy(., prop = survey_mean(na.rm = TRUE))
12: summarize(., prop = survey_mean(na.rm = TRUE))
13: mutate(., prop = prop * 100)
14: des %>% group_by_at(c(by_vars, "item", "resp")) %>% summarize(prop = survey_mean(na.rm = TRUE)) %>% mutate(prop = prop * 100)
15: table_weightedpct(df = df_adults_noNA, vars_ids = "PSU", vars_strata = "strata", vars_weights = "weight", formula_vars = paste0("EF", 1:12), formula_vars_levels = 1:5, by_vars = "disability_cat", spread_key = NULL, spread_value = "prop", arrange_vars = NULL, willfilter = NULL)
16: eval(expr, envir)
17: eval(expr, envir)
18: withVisible(eval(expr, envir))
19: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$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$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
20: eval(call)
21: eval(call)
22: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
23: doWithOneRestart(return(expr), restart)
24: withOneRestart(expr, restarts[[1L]])
25: withRestartList(expr, restarts[-nr])
26: doWithOneRestart(return(expr), restart)
27: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
28: withRestartList(expr, restarts)
29: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
30: evaluate::evaluate(...)
31: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
32: in_dir(input_dir(), expr)
33: 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$render, options)))
34: eng_r(options)
35: block_exec(params)
36: call_block(x)
37: process_group(group)
38: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
39: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
40: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
41: process_file(text, output)
42: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
43: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
44: vweave_rmarkdown(...)
45: engine$weave(file, quiet = quiet, encoding = enc)
46: doTryCatch(return(expr), name, parentenv, handler)
47: tryCatchOne(expr, names, parentenv, handlers[[1L]])
48: tryCatchList(expr, classes, parentenv, handlers)
49: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)), domain = NA)})
50: tools:::.buildOneVignette("c6_after_rasch_EN.Rmd", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/whomds.Rcheck/vign_test/whomds", TRUE, FALSE, "c6_after_rasch_EN", "UTF-8", "/home/hornik/tmp/scratch/RtmpVkhhFm/file2e3090492d6e53.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
--- re-building ‘c6_after_rasch_ES.Rmd’ using rmarkdown
*** caught segfault ***
address 0x294000001b4, cause 'memory not mapped'
Traceback:
1: .Call(dplyr_mask_eval_all_summarise, quo, private)
2: eval()
3: mask$eval_all_summarise(quo)
4: FUN(X[[i]], ...)
5: lapply(.x, .f, ...)
6: map(quosures, summarise_eval_one, mask = mask)
7: withCallingHandlers({ for (i in seq_along(dots)) { poke_error_context(dots, i, mask = mask) context_poke("column", old_current_column) dot <- dots[[i]] dot <- expand_pick(dot, mask) quosures <- expand_across(dot) quosures_results <- map(quosures, summarise_eval_one, mask = mask) for (k in seq_along(quosures)) { quo <- quosures[[k]] quo_data <- attr(quo, "dplyr:::data") quo_result <- quosures_results[[k]] if (is.null(quo_result)) { next } types_k <- quo_result$types chunks_k <- quo_result$chunks results_k <- quo_result$results if (!quo_data$is_named && is.data.frame(types_k)) { chunks_extracted <- .Call(dplyr_extract_chunks, chunks_k, types_k) types_k_names <- names(types_k) for (j in seq_along(chunks_extracted)) { mask$add_one(name = types_k_names[j], chunks = chunks_extracted[[j]], result = results_k[[j]]) } chunks <- append(chunks, chunks_extracted) types <- append(types, as.list(types_k)) results <- append(results, results_k) out_names <- c(out_names, types_k_names) } else { name <- dplyr_quosure_name(quo_data) mask$add_one(name = name, chunks = chunks_k, result = results_k) chunks <- append(chunks, list(chunks_k)) types <- append(types, list(types_k)) results <- append(results, list(results_k)) out_names <- c(out_names, name) } } } if (verb == "summarise") { .Call(dplyr_summarise_check_all_size_one, chunks, n_groups) group_sizes <- NULL } else { group_sizes <- .Call(dplyr_reframe_recycle_horizontally_in_place, chunks, results, n_groups) for (i in seq_along(chunks)) { if (is.null(results[[i]])) { results[[i]] <- vec_c(!!!chunks[[i]], .ptype = types[[i]]) } } }}, error = function(cnd) { if (inherits(cnd, "dplyr:::reframe_incompatible_size")) { action <- "recycle" i <- cnd$dplyr_error_data$index_expression } else if (inherits(cnd, "dplyr:::summarise_incompatible_size")) { action <- "compute" i <- cnd$dplyr_error_data$index_expression } else { action <- "compute" i <- i } handler <- dplyr_error_handler(dots = dots, mask = mask, bullets = summarise_bullets, error_call = error_call, action = action) handler(cnd)}, warning = dplyr_warning_handler(state = warnings_state, mask = mask, error_call = error_call))
8: summarise_cols(.data, dplyr_quosures(...), by, "summarise")
9: summarise.grouped_df(.data$variables, !!!.dots, .groups = .groups)
10: dplyr::summarise(.data$variables, !!!.dots, .groups = .groups)
11: summarise.grouped_svy(., prop = survey_mean(na.rm = TRUE))
12: summarize(., prop = survey_mean(na.rm = TRUE))
13: mutate(., prop = prop * 100)
14: des %>% group_by_at(c(by_vars, "item", "resp")) %>% summarize(prop = survey_mean(na.rm = TRUE)) %>% mutate(prop = prop * 100)
15: table_weightedpct(df = df_adults_noNA, vars_ids = "PSU", vars_strata = "strata", vars_weights = "weight", formula_vars = paste0("EF", 1:12), formula_vars_levels = 1:5, by_vars = "disability_cat", spread_key = NULL, spread_value = "prop", arrange_vars = NULL, willfilter = NULL)
16: eval(expr, envir)
17: eval(expr, envir)
18: withVisible(eval(expr, envir))
19: withCallingHandlers(code, error = function (e) rlang::entrace(e), 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)})
20: eval(call)
21: eval(call)
22: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
23: doWithOneRestart(return(expr), restart)
24: withOneRestart(expr, restarts[[1L]])
25: withRestartList(expr, restarts[-nr])
26: doWithOneRestart(return(expr), restart)
27: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
28: withRestartList(expr, restarts)
29: withRestarts(with_handlers({ for (expr in tle$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)
30: evaluate::evaluate(...)
31: 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$render, options))
32: in_dir(input_dir(), expr)
33: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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)))
34: eng_r(options)
35: block_exec(params)
36: call_block(x)
37: process_group(group)
38: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
39: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
40: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), 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)
41: process_file(text, output)
42: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
43: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
44: vweave_rmarkdown(...)
45: engine$weave(file, quiet = quiet, encoding = enc)
46: doTryCatch(return(expr), name, parentenv, handler)
47: tryCatchOne(expr, names, parentenv, handlers[[1L]])
48: tryCatchList(expr, classes, parentenv, handlers)
49: tryCatch({ engine$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) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)), domain = NA)})
50: tools:::.buildOneVignette("c6_after_rasch_ES.Rmd", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/whomds.Rcheck/vign_test/whomds", TRUE, FALSE, "c6_after_rasch_ES", "UTF-8", "/home/hornik/tmp/scratch/RtmpVkhhFm/file2e3090443be890.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
SUMMARY: processing the following files failed:
‘c6_after_rasch_EN.Rmd’ ‘c6_after_rasch_ES.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc