Last updated on 2026-08-09 20:50:14 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.3 | 16.64 | 147.90 | 164.54 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.3.3 | 12.62 | 107.47 | 120.09 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.3.3 | 14.00 | 89.40 | 103.40 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.3.3 | 13.00 | 90.91 | 103.91 | ERROR | |
| r-devel-windows-x86_64 | 0.3.3 | 28.00 | 150.00 | 178.00 | OK | |
| r-patched-linux-x86_64 | 0.3.3 | 17.84 | 140.60 | 158.44 | OK | |
| r-release-linux-x86_64 | 0.3.3 | 16.80 | 140.77 | 157.57 | OK | |
| r-release-macos-arm64 | 0.3.3 | 5.00 | 34.00 | 39.00 | OK | |
| r-release-macos-x86_64 | 0.3.3 | 13.00 | 176.00 | 189.00 | OK | |
| r-release-windows-x86_64 | 0.3.3 | 27.00 | 157.00 | 184.00 | OK | |
| r-oldrel-macos-arm64 | 0.3.3 | 4.00 | 38.00 | 42.00 | OK | |
| r-oldrel-macos-x86_64 | 0.3.3 | 17.00 | 374.00 | 391.00 | OK | |
| r-oldrel-windows-x86_64 | 0.3.3 | 30.00 | 205.00 | 235.00 | OK |
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’ [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.
autonomy: ..............................SS..................................
bma-auto-select: ........S............S....
> test-bma.R: PIP Post Mean Post SD Cond.Pos.Sign Idx
> test-bma.R: se 0.176 0.078977171 0.301639505 1 1
> test-bma.R: moderator2 0.152 0.003282200 0.015080483 1 3
> test-bma.R: moderator1 0.112 -0.001213489 0.006267098 0 2
> test-bma.R:
> test-bma.R: Mean no. regressors Draws Burnins Time
> test-bma.R: "0.4400" "500" "100" "0.0450542 secs"
> test-bma.R: No. models visited Modelspace 2^K % visited % Topmodels
> test-bma.R: "193" "8" "2412" "100"
> test-bma.R: Corr PMP No. Obs. Model Prior g-Prior
> test-bma.R: "0.9971" "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 0.0450542 secs
bma: ............................
box-plot-study-label: ..
> 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.
bma-collinearity: .................................................
data-column-resolution: ................................................
data-column-recognition: .......................................................................................
data-compute: ......
data-config-defaults: ...............................................
> test-data-config-resolve.R: i Reading data from '/tmp/RtmpB5XFF8/working_dir/RtmpA9CIgd/file20461e70a84b76.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/RtmpB5XFF8/working_dir/RtmpHp9Q6D/callr-fun-2044051dbd348a"), 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/RtmpB5XFF8/working_dir/RtmpHp9Q6D/callr-fun-2044051dbd348a"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE), file = "/tmp/RtmpB5XFF8/working_dir/RtmpHp9Q6D/callr-rs-result-20440544f6dd32", compress = FALSE)
> test-data-preview.R: 43: base::withCallingHandlers({ { NULL NULL } base::saveRDS(base::do.call(base::do.call, base::c(base::readRDS("/tmp/RtmpB5XFF8/working_dir/RtmpHp9Q6D/callr-fun-2044051dbd348a"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv,
> test-data-preview.R: quote = TRUE), file = "/tmp/RtmpB5XFF8/working_dir/RtmpHp9Q6D/callr-rs-result-20440544f6dd32",
> test-data-preview.R: 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$record_exception(e2) } base::saveRDS(base::list("error", e2, e), file = base::paste0("/tmp/RtmpB5XFF8/working_dir/RtmpHp9Q6D/callr-rs-result-20440544f6dd32", ".error")) }}, interrupt = function(e) { { callr_data <- base::as.environment("tools:callr")$`__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/RtmpB5XFF8/working_dir/RtmpHp9Q6D/callr-rs-result-20440544f6dd32", ".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$write_fd(3L, data) if (base::inherits(e, "cli_message") && !base::is.null(base::findRestart("cli_message_handled"))) { base::invokeRestart("cli_message_handled") } else if (base::inherits(e, "message") && !base::is.null(base::findRestart("muffleMessage"))) { base::invokeRestart("muffleMessage") } })})
> test-data-preview.R: 44: doTryCatch(return(expr), name, parentenv, handler)
> test-data-preview.R: 45: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> test-data-preview.R: 46: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
> test-data-preview.R: 47: doTryCatch(return(expr), name, parentenv, handler)
> test-data-preview.R: 48: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
> test-data-preview.R: 49: tryCatchList(expr, classes, parentenv, handlers)
> test-data-preview.R: 50: base::tryCatch(base::withCallingHandlers({ { NULL NULL } base::saveRDS(base::do.call(base::do.call, base::c(base::readRDS("/tmp/RtmpB5XFF8/working_dir/RtmpHp9Q6D/callr-fun-2044051dbd348a"), base::list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv, quote = TRUE), file = "/tmp/RtmpB5XFF8/working_dir/RtmpHp9Q6D/callr-rs-result-20440544f6dd32", compress = FALSE) base::flush(base::stdout()) base::flush(base::stderr()) { NULL NULL } base::invisible()}, error = function(e) { { callr_data <- base::as.environment("tools:callr")$`__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/RtmpB5XFF8/working_dir/RtmpHp9Q6D/callr-rs-result-20440544f6dd32", ".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$record_exception(e2) } base::saveRDS(base::list("error", e2, e), file = base::paste0("/tmp/RtmpB5XFF8/working_dir/RtmpHp9Q6D/callr-rs-result-20440544f6dd32", ".error")) }}, callr_message = function(e) { base::try({ callr_data <- base::as.environment("tools:callr")$`__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-gcc