CRAN Package Check Results for Maintainer ‘Ger Inberg <g.inberg at erasmusmc.nl>’

Last updated on 2025-04-12 20:52:14 CEST.

Package	ERROR	OK
DrugExposureDiagnostics	1	14
FeatureExtraction		14

Package DrugExposureDiagnostics

Current CRAN status: ERROR: 1, OK: 14

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

Package FeatureExtraction

Current CRAN status: OK: 14