CRAN Package Check Results for Maintainer ‘Petr Čala <61505008 at fsv.cuni.cz>’

Last updated on 2026-08-13 11:51:33 CEST.

Package	OK	ERROR	Other
artma	11	2	1
climenu	13

Package artma

Current CRAN status: OK: 11, ERROR: 2, Other: 1

Additional issues

clang-ASAN

Version: 0.3.3
Check: tests
Result: ERROR Running ‘testthat.R’ [22s/14s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # nolint start: undesirable_function_linter. > library(testthat) > library(artma) > # nolint end: undesirable_function_linter. > > testthat::test_check("artma", reporter = "summary") Starting 2 test processes. bma-auto-select: ........S............S.... autonomy: ..............................SS.................................. > test-bma.R: PIP Post Mean Post SD Cond.Pos.Sign Idx > test-bma.R: se 0.180 0.080833583 0.304824941 1 1 > test-bma.R: moderator2 0.160 0.003473794 0.015469847 1 3 > test-bma.R: moderator1 0.156 -0.001691547 0.007343082 0 2 > test-bma.R: > test-bma.R: Mean no. regressors > test-bma.R: Draws Burnins Time > test-bma.R: "0.4960" "500" "100" "0.05747795 secs" > test-bma.R: No. models visited Modelspace 2^K % visited % Topmodels > test-bma.R: "191" "8" "2388" "100" > test-bma.R: Corr PMP No. Obs. Model Prior g-Prior > test-bma.R: "0.9996" "50" "uniform / 1.5" "UIP" > test-bma.R: Shrinkage-Stats > test-bma.R: "Av=0.9804" > test-bma.R: > test-bma.R: Time difference of 0.05747795 secs bma: ............................ box-plot-study-label: .. bma-collinearity: ................................................. > test-data-auto-detection-confirmation.R: What would you like to do? > test-data-auto-detection-confirmation.R: What would you like to do? data-auto-detection-confirmation: ..................W.W. data-column-resolution: ................................................ data-column-recognition: ....................................................................................... data-compute: ...... data-config-defaults: ............................................... > test-data-config-resolve.R: i Reading data from '/tmp/Rtmp8xUXXQ/working_dir/RtmpMoCmFc/file2232c0646df650.csv' > test-data-config-resolve.R: v Data read successfully: 1000 rows, 5 columns data-config-resolve: ..................S......... > test-data-interactive-mapping.R: > test-data-interactive-mapping.R: -- Column Mapping Summary -- > test-data-interactive-mapping.R: > test-data-interactive-mapping.R: study_id (required) -> "study_name" > test-data-interactive-mapping.R: effect (required) -> "effect" > test-data-interactive-mapping.R: ! Missing required columns: se, n_obs > test-data-interactive-mapping.R: Saving column mapping to options > test-data-interactive-mapping.R: v Column mapping saved data-interactive-mapping: ....................... data-index: . > test-data-preview.R: > test-data-preview.R: *** caught segfault *** > test-data-preview.R: address (nil), cause 'memory not mapped' > test-data-preview.R: > test-data-preview.R: Traceback: > test-data-preview.R: 1: utils::View(x, title = title) > test-data-preview.R: 2: doTryCatch(return(expr), name, parentenv, handler) > test-data-preview.R: 3: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > test-data-preview.R: 4: tryCatchList(expr, classes, parentenv, handlers) > test-data-preview.R: 5: tryCatch(utils::View(x, title = title), error = function(e) invisible(NULL)) > test-data-preview.R: 6: view_if_available(data, title = "Preview: data") > test-data-preview.R: 7: artma::data.preview(df, preprocess = FALSE) > test-data-preview.R: 8: eval(code, test_env) > test-data-preview.R: 9: eval(code, test_env) > test-data-preview.R: 10: 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) > test-data-preview.R: 11: doTryCatch(return(expr), name, parentenv, handler) > test-data-preview.R: 12: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > test-data-preview.R: 13: tryCatchList(expr, classes, parentenv, handlers) > test-data-preview.R: 14: 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) > test-data-preview.R: 15: doWithOneRestart(return(expr), restart) > test-data-preview.R: 16: withOneRestart(expr, restarts[[1L]]) > test-data-preview.R: 17: 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() { }) > test-data-preview.R: 18: test_code(code, parent.frame()) > test-data-preview.R: 19: test_that("data.preview with data frame and preprocess FALSE returns invisibly", { withr::local_options(list(artma.verbose = 0)) df <- data.frame(study_id = c("A", "B"), effect = c(0.5, 0.3), se = c(0.1, 0.15), n_obs = c(100, 200)) out <- artma::data.preview(df, preprocess = FALSE) expect_null(out) expect_invisible(artma::data.preview(df, preprocess = FALSE)) }) > test-data-preview.R: 20: eval(code, test_env) > test-data-preview.R: 21: eval(code, test_env) > test-data-preview.R: 22: 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) > test-data-preview.R: 23: doTryCatch(return(expr), name, parentenv, handler) > test-data-preview.R: 24: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > test-data-preview.R: 25: tryCatchList(expr, classes, parentenv, handlers) > test-data-preview.R: 26: 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) > test-data-preview.R: 27: doWithOneRestart(return(expr), restart) > test-data-preview.R: 28: withOneRestart(expr, restarts[[1L]]) > test-data-preview.R: 29: 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() { }) > test-data-preview.R: 30: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) > test-data-preview.R: 31: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call) > test-data-preview.R: 32: test_one_file(path, env = the$testing_env, shuffle = shuffle) > test-data-preview.R: 33: doTryCatch(return(expr), name, parentenv, handler) > test-data-preview.R: 34: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > test-data-preview.R: 35: tryCatchList(expr, classes, parentenv, handlers) > test-data-preview.R: 36: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) > test-data-preview.R: 37: with_reporter(multi, test_one_file(path, env = the$testing_env, shuffle = shuffle)) > test-data-preview.R: 38: asNamespace("testthat")$queue_task(path, shuffle) > test-data-preview.R: 39: (function (path, shuffle) { asNamespace("testthat")$queue_task(path, shuffle)})(base::quote("test-data-preview.R"), base::quote(FALSE)) > test-data-preview.R: 40: (function (what, args, quote = FALSE, envir = parent.frame()) { if (!is.list(args)) stop("second argument must be a list") if (quote) args <- lapply(args, enquote) .Internal(do.call(what, args, envir))})(base::quote(function (path, shuffle) { asNamespace("testthat")$queue_task(path, shuffle)}), base::quote(list("test-data-preview.R", FALSE)), envir = base::quote(<environment>), quote = base::quote(TRUE)) > test-data-preview.R: 41: base::do.call(base::do.call, base::c(base::readRDS("/tmp/Rtmp8xUXXQ/working_dir/Rtmpwyx15G/callr-fun-222c5d3d4860f4"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE) > test-data-preview.R: 42: base::saveRDS(base::do.call(base::do.call, base::c(base::readRDS("/tmp/Rtmp8xUXXQ/working_dir/Rtmpwyx15G/callr-fun-222c5d3d4860f4"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE), file = "/tmp/Rtmp8xUXXQ/working_dir/Rtmpwyx15G/callr-rs-result-222c5d59daf7a5", compress = FALSE) > test-data-preview.R: 43: base::withCallingHandlers({ { NULL NULL } base::saveRDS(base::do.call(base::do.call, base::c(base::readRDS("/tmp/Rtmp8xUXXQ/working_dir/Rtmpwyx15G/callr-fun-222c5d3d4860f4"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE), file = "/tmp/Rtmp8xUXXQ/working_dir/Rtmpwyx15G/callr-rs-result-222c5d59daf7a5", compress = FALSE) base::flush(base::stdout()) base::flush(base::stderr()) { NULL NULL } base::invisible()}, error = function(e) { { callr_data <- base::as.environment("tools:callr")$`__callr_data__` err <- callr_data$err if (FALSE) { base::assign(".Traceback", base::.traceback(4), envir = callr_data) utils::dump.frames("__callr_dump__") base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data) base::rm("__callr_dump__", envir = .GlobalEnv) } e <- err$process_call(e) e2 <- err$new_error("error in callr subprocess") class <- base::class class(e2) <- base::c("callr_remote_error", class(e2)) e2 <- err$add_trace_back(e2) cut <- base::which(e2$trace$scope == "global")[1] if (!base::is.na(cut)) { e2$trace <- e2$trace[-(1:cut), ] } if (callr_data$has_otel) { callr_data$otel_span$record_exception(e2) } base::saveRDS(base::list("error", e2, e), file = base::paste0("/tmp/Rtmp8xUXXQ/working_dir/Rtmpwyx15G/callr-rs-result-222c5d59daf7a5", ".error")) }}, interrupt = function(e) { { callr_data <- base::as.environment("tools:callr")$`__callr_data__` err <- callr_data$err if (FALSE) { base::assign(".Traceback", base::.traceback(4), envir = callr_data) utils::dump.frames("__callr_dump__") base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data) base::rm("__callr_dump__", envir = .GlobalEnv) } e <- err$process_call(e) e2 <- err$new_error("error in callr subprocess") class <- base::class class(e2) <- base::c("callr_remote_error", class(e2)) e2 <- err$add_trace_back(e2) cut <- base::which(e2$trace$scope == "global")[1] if (!base::is.na(cut)) { e2$trace <- e2$trace[-(1:cut), ] } if (callr_data$has_otel) { > test-data-preview.R: callr_data$otel_span$record_exception(e2) } base::saveRDS(base::list("error", e2, e), file = base::paste0("/tmp/Rtmp8xUXXQ/working_dir/Rtmpwyx15G/callr-rs-result-222c5d59daf7a5", ".error")) }}, callr_message = function(e) { base::try({ callr_data <- base::as.environment("tools:callr")$`__callr_data__` pxlib <- callr_data$pxlib if (base::is.null(e$code)) { e$code <- "301" } msg <- base::paste0("base64::", pxlib$base64_encode(base::serialize(e, NULL))) data <- base::paste0(e$code, " ", base::nchar(msg), "\n", msg) if (callr_data$has_otel) { callr_data$otel_span$add_event("callr message", attributes = list(status_code = e$code)) } pxlib$write_fd(3L, data) if (base::inherits(e, "cli_message") && !base::is.null(base::findRestart("cli_message_handled"))) { base::invokeRestart("cli_message_handled") } else if (base::inherits(e, "message") && !base::is.null(base::findRestart("muffleMessage"))) { base::invokeRestart("muffleMessage") } })}) > test-data-preview.R: 44: doTryCatch(return(expr), name, parentenv, handler) > test-data-preview.R: 45: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > test-data-preview.R: 46: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) > test-data-preview.R: 47: doTryCatch(return(expr), name, parentenv, handler) > test-data-preview.R: 48: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) > test-data-preview.R: 49: tryCatchList(expr, classes, parentenv, handlers) > test-data-preview.R: 50: base::tryCatch(base::withCallingHandlers({ { NULL NULL } base::saveRDS(base::do.call(base::do.call, base::c(base::readRDS("/tmp/Rtmp8xUXXQ/working_dir/Rtmpwyx15G/callr-fun-222c5d3d4860f4"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE), file = "/tmp/Rtmp8xUXXQ/working_dir/Rtmpwyx15G/callr-rs-result-222c5d59daf7a5", compress = FALSE) base::flush(base::stdout()) base::flush(base::stderr()) { NULL NULL } base::invisible()}, error = function(e) { { callr_data <- base::as.environment("tools:callr")$`__callr_data__` err <- callr_data$err if (FALSE) { base::assign(".Traceback", base::.traceback(4), envir = callr_data) utils::dump.frames("__callr_dump__") base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data) base::rm("__callr_dump__", envir = .GlobalEnv) } e <- err$process_call(e) e2 <- err$new_error("error in callr subprocess") class <- base::class class(e2) <- base::c("callr_remote_error", class(e2)) e2 <- err$add_trace_back(e2) cut <- base::which(e2$trace$scope == "global")[1] if (!base::is.na(cut)) { e2$trace <- e2$trace[-(1:cut), ] } if (callr_data$has_otel) { callr_data$otel_span$record_exception(e2) } base::saveRDS(base::list("error", e2, e), file = base::paste0("/tmp/Rtmp8xUXXQ/working_dir/Rtmpwyx15G/callr-rs-result-222c5d59daf7a5", ".error")) }}, interrupt = function(e) { { callr_data <- base::as.environment("tools:callr")$`__callr_data__` err <- callr_data$err if (FALSE) { base::assign(".Traceback", base::.traceback(4), envir = callr_data) utils::dump.frames("__callr_dump__") base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data) base::rm("__callr_dump__", envir = .GlobalEnv) } e <- err$process_call(e) e2 <- err$new_error("error in callr subprocess") class <- base::class class(e2) <- base::c("callr_remote_error", class(e2)) e2 <- err$add_trace_back(e2) cut <- base::which(e2$trace$scope == "global")[1] if (!base::is.na(cut)) { e2$trace <- e2$trace[-(1:cut), ] } if (callr_data$has_otel) { callr_data$otel_span$record_exception(e2) } base::saveRDS(base::list("error", e2, e), file = base::paste0("/tmp/Rtmp8xUXXQ/working_dir/Rtmpwyx15G/callr-rs-result-222c5d59daf7a5", ".error")) }}, callr_message = function(e) { base::try({ callr_data <- base::as.environment("tools:callr")$`__callr_data__` pxlib <- callr_data$pxlib if (base::is.null(e$code)) { e$code <- "301" } msg <- base::paste0("base64::", pxlib$base64_encode(base::serialize(e, NULL))) data <- base::paste0(e$code, " ", base::nchar(msg), "\n", msg) if (callr_data$has_otel) { callr_data$otel_span$add_event("callr message", attributes = list(status_code = e$code)) } pxlib$write_fd(3L, data) if (base::inherits(e, "cli_message") && !base::is.null(base::findRestart("cli_message_handled"))) { base::invokeRestart("cli_message_handled") } else if (base::inherits(e, "message") && !base::is.null(base::findRestart("muffleMessage"))) { base::invokeRestart("muffleMessage") } })}), error = function(e) { { NULL NULL } if (FALSE) { base::try(base::stop(e)) } if (FALSE) { base::q(save = "no", status = 1) } base::invisible()}, interrupt = function(e) { { NULL NULL } if (FALSE) { base::q(save = "no", status = 1) } base::invisible()}) > test-data-preview.R: An irrecoverable exception occurred. R is aborting now ... data-preprocess: ....W..................... > test-data-smart-detection.R: i Removing 1 empty column: "empty" > test-data-smart-detection.R: ! Found duplicate column names: "name"Making names unique... > test-data-smart-detection.R: i Removing 2 trailing empty rows > test-data-smart-detection.R: i Removing 2 empty columns: "empty1" and "empty2" > test-data-smart-detection.R: i Removing 2 trailing empty rows data-smart-detection: ................................. Error: ! testthat subprocess exited in file 'test-data-preview.R'. Caused by error: ! R session crashed with exit code -11 Backtrace: ▆ 1. └─testthat::test_check("artma", reporter = "summary") 2. └─testthat::test_dir(...) 3. └─testthat:::test_files(...) 4. └─testthat:::test_files_parallel(...) 5. ├─withr::with_dir(...) 6. │ └─base::force(code) 7. ├─testthat::with_reporter(...) 8. │ └─base::tryCatch(...) 9. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. └─testthat:::parallel_event_loop_chunky(queue, reporters, ".") 13. └─queue$poll(Inf) 14. └─base::lapply(...) 15. └─testthat (local) FUN(X[[i]], ...) 16. └─private$handle_error(msg, i) 17. └─cli::cli_abort(...) 18. └─rlang::abort(...) Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.3.3
Check: tests
Result: ERROR Running ‘testthat.R’ [21s/14s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # nolint start: undesirable_function_linter. > library(testthat) > library(artma) > # nolint end: undesirable_function_linter. > > testthat::test_check("artma", reporter = "summary") Starting 2 test processes. autonomy: ..............................SS.................................. bma-auto-select: ........S............S.... > test-bma.R: PIP Post Mean Post SD Cond.Pos.Sign Idx > test-bma.R: se 0.204 0.091392700 0.322780027 1 1 > test-bma.R: moderator1 0.156 -0.001686166 0.007336965 0 2 > test-bma.R: moderator2 0.122 0.002648029 0.013588583 1 3 > test-bma.R: > test-bma.R: Mean no. regressors > test-bma.R: Draws Burnins Time > test-bma.R: "0.4820" "500" "100" "0.04898906 secs" > test-bma.R: No. models visited Modelspace 2^K % visited % Topmodels > test-bma.R: "176" "8" "2200" "100" > test-bma.R: Corr PMP No. Obs. Model Prior g-Prior > test-bma.R: "0.9967" "50" "uniform / 1.5" "UIP" > test-bma.R: Shrinkage-Stats > test-bma.R: "Av=0.9804" > test-bma.R: > test-bma.R: Time difference of 0.04898906 secs bma: ............................ box-plot-study-label: .. > test-data-auto-detection-confirmation.R: What would you like to do? bma-collinearity: ................................................. > test-data-auto-detection-confirmation.R: What would you like to do? data-auto-detection-confirmation: ..................W.W. data-column-resolution: ................................................ data-compute: ...... data-column-recognition: ....................................................................................... data-config-defaults: ............................................... > test-data-config-resolve.R: i Reading data from '/tmp/RtmpBrg07M/working_dir/RtmpFpt2Fo/file27d74969b6625b.csv' > test-data-config-resolve.R: v Data read successfully: 1000 rows, 5 columns data-config-resolve: ..................S......... > test-data-interactive-mapping.R: > test-data-interactive-mapping.R: -- Column Mapping Summary -- > test-data-interactive-mapping.R: > test-data-interactive-mapping.R: study_id (required) -> "study_name" > test-data-interactive-mapping.R: effect (required) -> "effect" > test-data-interactive-mapping.R: ! Missing required columns: se, n_obs > test-data-interactive-mapping.R: Saving column mapping to options > test-data-interactive-mapping.R: v Column mapping saved data-index: . data-interactive-mapping: ....................... > test-data-preview.R: > test-data-preview.R: *** caught segfault *** > test-data-preview.R: address (nil), cause 'memory not mapped' > test-data-preview.R: > test-data-preview.R: Traceback: > test-data-preview.R: 1: utils::View(x, title = title) > test-data-preview.R: 2: doTryCatch(return(expr), name, parentenv, handler) > test-data-preview.R: 3: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > test-data-preview.R: 4: tryCatchList(expr, classes, parentenv, handlers) > test-data-preview.R: 5: tryCatch(utils::View(x, title = title), error = function(e) invisible(NULL)) > test-data-preview.R: 6: view_if_available(data, title = "Preview: data") > test-data-preview.R: 7: artma::data.preview(df, preprocess = FALSE) > test-data-preview.R: 8: eval(code, test_env) > test-data-preview.R: 9: eval(code, test_env) > test-data-preview.R: 10: 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) > test-data-preview.R: 11: doTryCatch(return(expr), name, parentenv, handler) > test-data-preview.R: 12: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > test-data-preview.R: 13: tryCatchList(expr, classes, parentenv, handlers) > test-data-preview.R: 14: 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) > test-data-preview.R: 15: doWithOneRestart(return(expr), restart) > test-data-preview.R: 16: withOneRestart(expr, restarts[[1L]]) > test-data-preview.R: 17: 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() { }) > test-data-preview.R: 18: test_code(code, parent.frame()) > test-data-preview.R: 19: test_that("data.preview with data frame and preprocess FALSE returns invisibly", { withr::local_options(list(artma.verbose = 0)) df <- data.frame(study_id = c("A", "B"), effect = c(0.5, 0.3), se = c(0.1, 0.15), n_obs = c(100, 200)) out <- artma::data.preview(df, preprocess = FALSE) expect_null(out) expect_invisible(artma::data.preview(df, preprocess = FALSE)) }) > test-data-preview.R: 20: eval(code, test_env) > test-data-preview.R: 21: eval(code, test_env) > test-data-preview.R: 22: 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) > test-data-preview.R: 23: doTryCatch(return(expr), name, parentenv, handler) > test-data-preview.R: 24: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > test-data-preview.R: 25: tryCatchList(expr, classes, parentenv, handlers) > test-data-preview.R: 26: 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) > test-data-preview.R: 27: doWithOneRestart(return(expr), restart) > test-data-preview.R: 28: withOneRestart(expr, restarts[[1L]]) > test-data-preview.R: 29: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations > test-data-preview.R: if (snapshot_skipped) { > test-data-preview.R: skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$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() { }) > test-data-preview.R: 30: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) > test-data-preview.R: 31: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call) > test-data-preview.R: 32: test_one_file(path, env = the$testing_env, shuffle = shuffle) > test-data-preview.R: 33: doTryCatch(return(expr), name, parentenv, handler) > test-data-preview.R: 34: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > test-data-preview.R: 35: tryCatchList(expr, classes, parentenv, handlers) > test-data-preview.R: 36: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) > test-data-preview.R: 37: with_reporter(multi, test_one_file(path, env = the$testing_env, shuffle = shuffle)) > test-data-preview.R: 38: asNamespace("testthat")$queue_task(path, shuffle) > test-data-preview.R: 39: (function (path, shuffle) { asNamespace("testthat")$queue_task(path, shuffle)})(base::quote("test-data-preview.R"), base::quote(FALSE)) > test-data-preview.R: 40: (function (what, args, quote = FALSE, envir = parent.frame()) { if (!is.list(args)) stop("second argument must be a list") if (quote) args <- lapply(args, enquote) .Internal(do.call(what, args, envir))})(base::quote(function (path, shuffle) { asNamespace("testthat")$queue_task(path, shuffle)}), base::quote(list("test-data-preview.R", FALSE)), envir = base::quote(<environment>), quote = base::quote(TRUE)) > test-data-preview.R: 41: base::do.call(base::do.call, base::c(base::readRDS("/tmp/RtmpBrg07M/working_dir/RtmphAiyAo/callr-fun-27d2befd4d393"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE) > test-data-preview.R: 42: base::saveRDS(base::do.call(base::do.call, base::c(base::readRDS("/tmp/RtmpBrg07M/working_dir/RtmphAiyAo/callr-fun-27d2befd4d393"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE), file = "/tmp/RtmpBrg07M/working_dir/RtmphAiyAo/callr-rs-result-27d2be1f11451d", compress = FALSE) > test-data-preview.R: 43: base::withCallingHandlers({ { NULL NULL } base::saveRDS(base::do.call(base::do.call, base::c(base::readRDS("/tmp/RtmpBrg07M/working_dir/RtmphAiyAo/callr-fun-27d2befd4d393"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE), file = "/tmp/RtmpBrg07M/working_dir/RtmphAiyAo/callr-rs-result-27d2be1f11451d", compress = FALSE) base::flush(base::stdout()) base::flush(base::stderr()) { NULL NULL } base::invisible()}, error = function(e) { { callr_data <- base::as.environment("tools:callr")$`__callr_data__` err <- callr_data$err if (FALSE) { base::assign(".Traceback", base::.traceback(4), envir = callr_data) utils::dump.frames("__callr_dump__") base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data) base::rm("__callr_dump__", envir = .GlobalEnv) } e <- err$process_call(e) e2 <- err$new_error("error in callr subprocess") class <- base::class class(e2) <- base::c("callr_remote_error", class(e2)) e2 <- err$add_trace_back(e2) cut <- base::which(e2$trace$scope == "global")[1] if (!base::is.na(cut)) { e2$trace <- e2$trace[-(1:cut), ] } if (callr_data$has_otel) { callr_data$otel_span$record_exception(e2) } base::saveRDS(base::list("error", e2, e), file = base::paste0("/tmp/RtmpBrg07M/working_dir/RtmphAiyAo/callr-rs-result-27d2be1f11451d", ".error")) }}, interrupt = function(e) { { callr_data <- base::as.environment("tools:callr")$`__callr_data__` err <- callr_data$err if (FALSE) { base::assign(".Traceback", base::.traceback(4), envir = callr_data) utils::dump.frames("__callr_dump__") base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data) base::rm("__callr_dump__", envir = .GlobalEnv) } e <- err$process_call(e) e2 <- err$new_error("error in callr subprocess") class <- base::class class(e2) <- base::c("callr_remote_error", class(e2)) e2 <- err$add_trace_back(e2) cut <- base::which(e2$trace$scope == "global")[1] if (!base::is.na(cut)) { e2$trace <- e2$trace[-(1:cut), ] } if (callr_data$has_otel) { callr_data$otel_span$record_exception(e2) } base::saveRDS(base::list("error", e2, e), file = base::paste0("/tmp/RtmpBrg07M/working_dir/RtmphAiyAo/callr-rs-result-27d2be1f11451d", ".error")) }}, callr_message = function(e) { base::try({ callr_data <- base::as.environment("tools:callr")$`__callr_data__` pxlib <- callr_data$pxlib if (base::is.null(e$code)) { e$code <- "301" } msg <- base::paste0("base64::", pxlib$base64_encode(base::serialize(e, NULL))) data <- base::paste0(e$code, " ", base::nchar(msg), "\n", msg) if (callr_data$has_otel) { callr_data$otel_span$add_event("callr message", attributes = list(status_code = e$code)) } pxlib$write_fd(3L, data) if (base::inherits(e, "cli_message") && !base::is.null(base::findRestart("cli_message_handled"))) { base::invokeRestart("cli_message_handled") } else if (base::inherits(e, "message") && !base::is.null(base::findRestart("muffleMessage"))) { base::invokeRestart("muffleMessage") } })}) > test-data-preview.R: 44: doTryCatch(return(expr), name, parentenv, handler) > test-data-preview.R: 45: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > test-data-preview.R: 46: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) > test-data-preview.R: 47: doTryCatch(return(expr), name, parentenv, handler) > test-data-preview.R: 48: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) > test-data-preview.R: 49: tryCatchList(expr, classes, parentenv, handlers) > test-data-preview.R: 50: base::tryCatch(base::withCallingHandlers({ { NULL NULL } base::saveRDS(base::do.call(base::do.call, base::c(base::readRDS("/tmp/RtmpBrg07M/working_dir/RtmphAiyAo/callr-fun-27d2befd4d393"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE), file = "/tmp/RtmpBrg07M/working_dir/RtmphAiyAo/callr-rs-result-27d2be1f11451d", compress = FALSE) base::flush(base::stdout()) base::flush(base::stderr()) { NULL NULL } base::invisible()}, error = function(e) { { callr_data <- base::as.environment("tools:callr")$`__callr_data__` err <- callr_data$err if (FALSE) { base::assign(".Traceback", base::.traceback(4), envir = callr_data) utils::dump.frames("__callr_dump__") base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data) base::rm("__callr_dump__", envir = .GlobalEnv) } e <- err$process_call(e) e2 <- err$new_error("error in callr subprocess") class <- base::class class(e2) <- base::c("callr_remote_error", class(e2)) e2 <- err$add_trace_back(e2) cut <- base::which(e2$trace$scope == "global")[1] if (!base::is.na(cut)) { e2$trace <- e2$trace[-(1:cut), ] } if (callr_data$has_otel) { callr_data$otel_span$record_exception(e2) } base::saveRDS(base::list("error", e2, e), file = base::paste0("/tmp/RtmpBrg07M/working_dir/RtmphAiyAo/callr-rs-result-27d2be1f11451d", ".error")) }}, interrupt = function(e) { { callr_data <- base::as.environment("tools:callr")$`__callr_data__` err <- callr_data$err if (FALSE) { base::assign(".Traceback", base::.traceback(4), envir = callr_data) utils::dump.frames("__callr_dump__") base::assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data) base::rm("__callr_dump__", envir = .GlobalEnv) } e <- err$process_call(e) e2 <- err$new_error("error in callr subprocess") class <- base::class class(e2) <- base::c("callr_remote_error", class(e2)) e2 <- err$add_trace_back(e2) cut <- base::which(e2$trace$scope == "global")[1] if (!base::is.na(cut)) { e2$trace <- e2$trace[-(1:cut), ] } if (callr_data$has_otel) { callr_data$otel_span$record_exception(e2) } base::saveRDS(base::list("error", e2, e), file = base::paste0("/tmp/RtmpBrg07M/working_dir/RtmphAiyAo/callr-rs-result-27d2be1f11451d", ".error")) }}, callr_message = function(e) { base::try({ callr_data <- base::as.environment("tools:callr")$`__callr_data__` pxlib <- callr_data$pxlib if (base::is.null(e$code)) { e$code <- "301" } msg <- base::paste0("base64::", pxlib$base64_encode(base::serialize(e, NULL))) > test-data-preview.R: data <- base::paste0(e$code, " ", base::nchar(msg), "\n", msg) if (callr_data$has_otel) { callr_data$otel_span$add_event("callr message", attributes = list(status_code = e$code)) } pxlib$write_fd(3L, data) if (base::inherits(e, "cli_message") && !base::is.null(base::findRestart("cli_message_handled"))) { base::invokeRestart("cli_message_handled") } else if (base::inherits(e, "message") && !base::is.null(base::findRestart("muffleMessage"))) { base::invokeRestart("muffleMessage") } })}), error = function(e) { { NULL NULL } if (FALSE) { base::try(base::stop(e)) } if (FALSE) { base::q(save = "no", status = 1) } base::invisible()}, interrupt = function(e) { { NULL NULL } if (FALSE) { base::q(save = "no", status = 1) } base::invisible()}) > test-data-preview.R: An irrecoverable exception occurred. R is aborting now ... data-preprocess: ....W..................... > test-data-smart-detection.R: i Removing 1 empty column: "empty" > test-data-smart-detection.R: ! Found duplicate column names: "name"Making names unique... > test-data-smart-detection.R: i Removing 2 trailing empty rows > test-data-smart-detection.R: i Removing 2 empty columns: "empty1" and "empty2" > test-data-smart-detection.R: i Removing 2 trailing empty rows data-smart-detection: ................................. Error: ! testthat subprocess exited in file 'test-data-preview.R'. Caused by error: ! R session closed the process connection, killed Backtrace: ▆ 1. └─testthat::test_check("artma", reporter = "summary") 2. └─testthat::test_dir(...) 3. └─testthat:::test_files(...) 4. └─testthat:::test_files_parallel(...) 5. ├─withr::with_dir(...) 6. │ └─base::force(code) 7. ├─testthat::with_reporter(...) 8. │ └─base::tryCatch(...) 9. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. └─testthat:::parallel_event_loop_chunky(queue, reporters, ".") 13. └─queue$poll(Inf) 14. └─base::lapply(...) 15. └─testthat (local) FUN(X[[i]], ...) 16. └─private$handle_error(msg, i) 17. └─cli::cli_abort(...) 18. └─rlang::abort(...) Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Package climenu

Current CRAN status: OK: 13