Last updated on 2025-04-12 09:52:25 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.2 | 7.28 | 619.33 | 626.61 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.2 | 5.82 | 434.35 | 440.17 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.2 | 910.15 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.2 | 793.58 | ERROR | |||
| r-devel-macos-arm64 | 1.1.2 | 281.00 | OK | |||
| r-devel-macos-x86_64 | 1.1.2 | 274.00 | OK | |||
| r-devel-windows-x86_64 | 1.1.2 | 11.00 | 498.00 | 509.00 | OK | |
| r-patched-linux-x86_64 | 1.1.2 | 7.99 | 586.76 | 594.75 | OK | |
| r-release-linux-x86_64 | 1.1.2 | OK | ||||
| r-release-macos-arm64 | 1.1.2 | 204.00 | OK | |||
| r-release-macos-x86_64 | 1.1.2 | 288.00 | OK | |||
| r-release-windows-x86_64 | 1.1.2 | 13.00 | 734.00 | 747.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.2 | 232.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.1.2 | 377.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.1.2 | 13.00 | 680.00 | 693.00 | OK |
Version: 1.1.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [454s/589s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(DrugExposureDiagnostics)
>
> test_check("DrugExposureDiagnostics")
Attaching package: 'plotly'
The following object is masked from 'package:ggplot2':
last_plot
The following object is masked from 'package:stats':
filter
The following object is masked from 'package:graphics':
layout
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
population after earliestStartDate smaller than sample, sampling ignored
i The following estimates will be computed:
* daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2025-04-12 02:15:52.663292
v Summary finished, at 2025-04-12 02:15:54.545645
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
i The following estimates will be computed:
* daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2025-04-12 02:16:54.45439
===============>--------------- 2/4 group-strata combinations @ 2025-04-12 02...
==============================> 4/4 group-strata combinations @ 2025-04-12 02...
v Summary finished, at 2025-04-12 02:16:56.735484
population after earliestStartDate smaller than sample, sampling ignored
i The following estimates will be computed:
* daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2025-04-12 02:17:39.984514
===============>--------------- 2/4 group-strata combinations @ 2025-04-12 02...
==============================> 4/4 group-strata combinations @ 2025-04-12 02...
v Summary finished, at 2025-04-12 02:17:42.083955
i The following estimates will be computed:
* daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2025-04-12 02:17:48.355108
v Summary finished, at 2025-04-12 02:17:50.653531
Progress: getting descendant concepts of ingredient (1125315) used in database
Progress: getting descendant concepts of ingredient
Progress: adding drug strength info
Progress: limiting to concepts in the db
Progress: adding concept names
Overall time taken: 0 minutes and 3 seconds
Time taken: 0 minutes and 4 seconds
Progress: getting drug records for ingredient
Time taken: 0 minutes and 0 seconds
Progress: get concepts used
Time taken: 0 minutes and 0 seconds
Progress: sampling drug records
population after earliestStartDate smaller than sample, sampling ignored
Time taken: 0 minutes and 0 seconds
Progress: check drugsMissing
Time taken: 0 minutes and 5 seconds
Progress: check ExposureDuration
Time taken: 0 minutes and 0 seconds
Progress: check drugQuantity
Time taken: 0 minutes and 0 seconds
Finished
i The following estimates will be computed:
* daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2025-04-12 02:19:32.326187
===============>--------------- 2/4 group-strata combinations @ 2025-04-12 02...
==============================> 4/4 group-strata combinations @ 2025-04-12 02...
v Summary finished, at 2025-04-12 02:19:35.43372
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
i The following estimates will be computed:
* daily_dose: count_missing, percentage_missing, mean, sd, q05, q25, median, q75, q95, min, max
! Table is collected to memory as not all requested estimates are supported on the database side
> Start summary of data, at 2025-04-12 02:22:26.595744
v Summary finished, at 2025-04-12 02:22:28.390637
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
population after earliestStartDate smaller than sample, sampling ignored
*** caught segfault ***
address (nil), cause 'unknown'
Traceback:
1: rapi_execute(stmt, arrow, integer64)
2: withCallingHandlers(expr, condition = function(cnd) { { .__handler_frame__. <- TRUE .__setup_frame__. <- frame if (inherits(cnd, "message")) { except <- c("warning", "error") } else if (inherits(cnd, "warning")) { except <- "error" } else { except <- "" } } while (!is_null(cnd)) { if (inherits(cnd, "error")) { out <- handlers[[1L]](cnd) if (!inherits(out, "rlang_zap")) throw(out) } inherit <- .subset2(.subset2(cnd, "rlang"), "inherit") if (is_false(inherit)) { return() } cnd <- .subset2(cnd, "parent") }})
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(withCallingHandlers(expr, condition = function(cnd) { { .__handler_frame__. <- TRUE .__setup_frame__. <- frame if (inherits(cnd, "message")) { except <- c("warning", "error") } else if (inherits(cnd, "warning")) { except <- "error" } else { except <- "" } } while (!is_null(cnd)) { if (inherits(cnd, "error")) { out <- handlers[[1L]](cnd) if (!inherits(out, "rlang_zap")) throw(out) } inherit <- .subset2(.subset2(cnd, "rlang"), "inherit") if (is_false(inherit)) { return() } cnd <- .subset2(cnd, "parent") }}), stackOverflowError = handlers[[1L]])
7: rlang::try_fetch(rapi_execute(stmt, arrow, integer64), error = function(e) { rethrow_error_from_rapi(e, call)})
8: rethrow_rapi_execute(res@stmt_lst$ref, res@arrow, res@connection@bigint == "integer64")
9: duckdb_execute(res)
10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)
11: .local(conn, statement, ...)
12: dbSendQuery(conn, statement, ...)
13: dbSendQuery(conn, statement, ...)
14: dbSendStatement(conn, statement, ...)
15: dbSendStatement(conn, statement, ...)
16: dbExecute(con, sql, immediate = TRUE)
17: dbExecute(con, sql, immediate = TRUE)
18: withCallingHandlers(code, error = function(cnd) { msg <- c(msg, i = paste0("Using SQL: ", sql)) cli_abort(msg, parent = cnd, call = call, .envir = env)})
19: dbi_wrap(dbExecute(con, sql, immediate = TRUE), sql = sql, msg = msg, call = call, env = env)
20: db_execute(con, sql, "Can't save query to table {.table {format(name, con = con)}}.")
21: db_save_query.DBIConnection(con, ...)
22: eval_bare(expr((!!fun)(con, ...)))
23: dbplyr_fallback(con, "db_save_query", ...)
24: dbplyr_save_query(con, sql, table, ..., temporary = temporary, overwrite = overwrite)
25: withCallingHandlers(code, error = function(cnd) { cli_abort(msg, parent = cnd, call = call, .envir = env)})
26: with_transaction(con, in_transaction, "Can't copy query to table {.field {format(table, con = con)}}.", { table <- dbplyr_save_query(con, sql, table, ..., temporary = temporary, overwrite = overwrite) create_indexes(con, table, unique_indexes, unique = TRUE) create_indexes(con, table, indexes) if (analyze) dbplyr_analyze(con, table) })
27: db_compute.DBIConnection(x$src$con, name, sql, temporary = temporary, unique_indexes = unique_indexes, indexes = indexes, analyze = analyze, ...)
28: db_compute(x$src$con, name, sql, temporary = temporary, unique_indexes = unique_indexes, indexes = indexes, analyze = analyze, ...)
29: compute.tbl_sql(x, name = name, temporary = temporary, ...)
30: dplyr::compute(x, name = name, temporary = temporary, ...)
31: .computeQuery(x, name = name, temporary = temporary, schema = schema, overwrite = overwrite)
32: compute.db_cdm(addClass(keepClass(x), cl), name = name, temporary = temporary, overwrite = overwrite)
33: dplyr::compute(addClass(keepClass(x), cl), name = name, temporary = temporary, overwrite = overwrite)
34: compute.cdm_table(.)
35: dplyr::compute(.)
36: table %>% dplyr::compute()
37: computeDBQuery(table = dbConceptsTable, tablePrefix = tablePrefix, tableName = "_DED_concepts_3", cdm = cdm)
38: ingredientDescendantsInDb(cdm = cdm, ingredient = ingredient, verbose = verbose, tablePrefix = tablePrefix)
39: dplyr::compute(., name = "ingredient_concepts")
40: ingredientDescendantsInDb(cdm = cdm, ingredient = ingredient, verbose = verbose, tablePrefix = tablePrefix) %>% dplyr::compute(name = "ingredient_concepts")
41: executeChecksSingleIngredient(cdm = cdm, ingredient = ingredient, subsetToConceptId = subsetToConceptId, checks = checks, minCellCount = minCellCount, sampleSize = sample, tablePrefix = tablePrefix, earliestStartDate = earliestStartDate, verbose = verbose, byConcept = byConcept, exposureTypeId = exposureTypeId)
42: doTryCatch(return(expr), name, parentenv, handler)
43: tryCatchOne(expr, names, parentenv, handlers[[1L]])
44: tryCatchList(expr, classes, parentenv, handlers)
45: tryCatch({ ingredientResult <- executeChecksSingleIngredient(cdm = cdm, ingredient = ingredient, subsetToConceptId = subsetToConceptId, checks = checks, minCellCount = minCellCount, sampleSize = sample, tablePrefix = tablePrefix, earliestStartDate = earliestStartDate, verbose = verbose, byConcept = byConcept, exposureTypeId = exposureTypeId) if (!is.null(outputFolder)) { writeIngredientResultToDisk(resultList = ingredientResult, databaseId = databaseId, outputFolder = outputFolder, clearDBDir = (i == 1)) }}, error = function(e) { warning(e)})
46: executeChecks(cdm, ingredients = ingredients, subsetToConceptId = subsetToConceptId, checks = checks, sample = sample, tablePrefix = tablePrefix, earliestStartDate = earliestStartDate, verbose = verbose, exposureTypeId = exposureTypeId, minCellCount = minCellCount, outputFolder = outputFolder, databaseId = databaseId)
47: executeChecksMock(cdm = cdm, ingredients = 1125315, subsetToConceptId = c(-40162522, -19133768, -1127433, -40229134, -40231925, 1127078))
48: eval(code, test_env)
49: eval(code, test_env)
50: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
51: doTryCatch(return(expr), name, parentenv, handler)
52: tryCatchOne(expr, names, parentenv, handlers[[1L]])
53: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
58: test_code(desc, code, env = parent.frame(), reporter = reporter)
59: test_that("subset on specific concepts", { cdm <- mockDrugExposure() result_all <- executeChecksMock(cdm = cdm, ingredients = 1125315, subsetToConceptId = NULL) expect_true(all(result_all$conceptSummary$drug_concept_id %in% c(40162522, 19133768, 1127433, 1127078, 40229134, 40231925))) result_subset <- executeChecksMock(cdm = cdm, ingredients = 1125315, subsetToConceptId = 40162522) expect_true(all(result_subset$conceptSummary$drug_concept_id %in% c(40162522))) result_subset2 <- executeChecksMock(cdm = cdm, ingredients = 1125315, subsetToConceptId = c(40162522, 1127078)) expect_true(all(result_subset2$conceptSummary$drug_concept_id %in% c(40162522, 1127078))) result_subset3 <- executeChecksMock(cdm = cdm, ingredients = 1125315, subsetToConceptId = c(-40162522, -19133768, -1127433, -40229134, -40231925)) expect_true(all(result_subset3$conceptSummary$drug_concept_id == 1127078)) result_subset4 <- executeChecksMock(cdm = cdm, ingredients = 1125315, subsetToConceptId = c(-40162522, -19133768, -1127433, -40229134, -40231925, 1127078)) expect_true(identical(result_subset3, result_subset4)) expect_error(executeChecksMock(cdm = cdm, ingredients = 1125315, subsetToConceptId = c(-40162522, 40162522))) DBI::dbDisconnect(attr(cdm, "dbcon"), shutdown = TRUE)})
60: eval(code, test_env)
61: eval(code, test_env)
62: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
63: doTryCatch(return(expr), name, parentenv, handler)
64: tryCatchOne(expr, names, parentenv, handlers[[1L]])
65: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
66: doTryCatch(return(expr), name, parentenv, handler)
67: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
68: tryCatchList(expr, classes, parentenv, handlers)
69: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
70: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
71: source_file(path, env = env(env), desc = desc, error_call = error_call)
72: FUN(X[[i]], ...)
73: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
74: doTryCatch(return(expr), name, parentenv, handler)
75: tryCatchOne(expr, names, parentenv, handlers[[1L]])
76: tryCatchList(expr, classes, parentenv, handlers)
77: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
78: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
79: 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, error_call = error_call)
80: 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)
81: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
82: test_check("DrugExposureDiagnostics")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc