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Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(CDMConnector) > > test_check("CDMConnector") trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/GiBleed_5.3.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Download completed! Creating CDM database D:\temp\2025_09_16_00_55_17_23174\RtmpqyiPIW\file2dfd84e625335/GiBleed_5.3.zip Connecting using DuckDB driver i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [685ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [175ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [192ms] i Generating 3 cohorts i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [760ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [153ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [157ms] i Generating 3 cohorts i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [178ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [200ms] i Generating 1 cohort i Generating cohort (1/1) - deep_vein_thrombosis_01 v Generating cohort (1/1) - deep_vein_thrombosis_01 [183ms] i Generating 1 cohort i Generating cohort (1/1) - deep_vein_thrombosis_01 v Generating cohort (1/1) - deep_vein_thrombosis_01 [183ms] i Generating 2 cohorts i Generating 2 cohorts i Generating 2 cohorts i Generating 1 cohort i Generating cohort (1/1) - viral_sinusitus v Generating cohort (1/1) - viral_sinusitus [501ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_default v Generating cohort (1/1) - gibleed_default [263ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_default_with_descendants v Generating cohort (1/1) - gibleed_default_with_descendants [336ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_all v Generating cohort (1/1) - gibleed_all [277ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_all v Generating cohort (1/1) - gibleed_all [291ms] i Generating 1 cohort i Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 [181ms] i Generating 5 cohorts i Generating cohort (1/5) - gibleed_all v Generating cohort (1/5) - gibleed_all [335ms] i Generating cohort (2/5) - gibleed_default v Generating cohort (2/5) - gibleed_default [281ms] i Generating cohort (3/5) - gibleed_default_with_descendants v Generating cohort (3/5) - gibleed_default_with_descendants [429ms] i Generating cohort (4/5) - gibleed_all_end_10 v Generating cohort (4/5) - gibleed_all_end_10 [339ms] i Generating cohort (5/5) - gibleed_end_10 v Generating cohort (5/5) - gibleed_end_10 [578ms] Getting distinct count of concept relationship table Getting count of different relationship IDs in concept relationship table Getting join of concept and concept class computed to a temp table Getting concept table collected into memory Getting join of person and observation period collected into memory Getting summary of observation period start and end dates by gender concept id Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable', target signature 'duckdb_connection#Id'. "duckdb_connection#ANY" would also be valid i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [213ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [217ms] i Generating 3 cohorts i Generating cohort (1/3) - another_gibleed_male v Generating cohort (1/3) - another_gibleed_male [623ms] i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 [178ms] i Generating cohort (3/3) - another_deep_vein_thrombosis_01 v Generating cohort (3/3) - another_deep_vein_thrombosis_01 [160ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [787ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [163ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [164ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [537ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [150ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [186ms] i `EUNOMIA_DATA_FOLDER` set to: 'D:\temp\2025_09_16_00_55_17_23174\RtmpqyiPIW'. trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/GiBleed_5.3.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Download completed! Creating CDM database D:\temp\2025_09_16_00_55_17_23174\RtmpqyiPIW/GiBleed_5.3.zip Getting distinct count of concept relationship table Getting count of different relationship IDs in concept relationship table Getting join of concept and concept class computed to a temp table Getting concept table collected into memory Getting join of person and observation period collected into memory Getting summary of observation period start and end dates by gender concept id i Generating 1 cohort i Generating cohort (1/1) - gibleed_all v Generating cohort (1/1) - gibleed_all [300ms] i Computing hash for person (1/22) v Computing hash for observation_period (2/22) [63ms] i Computing hash for observation_period (2/22) v Computing hash for visit_occurrence (3/22) [82ms] i Computing hash for visit_occurrence (3/22) v Computing hash for condition_occurrence (4/22) [65ms] i Computing hash for condition_occurrence (4/22) v Computing hash for drug_exposure (5/22) [69ms] i Computing hash for drug_exposure (5/22) v Computing hash for procedure_occurrence (6/22) [57ms] i Computing hash for procedure_occurrence (6/22) v Computing hash for measurement (7/22) [61ms] i Computing hash for measurement (7/22) v Computing hash for observation (8/22) [67ms] i Computing hash for observation (8/22) v Computing hash for death (9/22) [86ms] i Computing hash for death (9/22) v Computing hash for location (10/22) [58ms] i Computing hash for location (10/22) v Computing hash for care_site (11/22) [60ms] i Computing hash for care_site (11/22) v Computing hash for provider (12/22) [58ms] i Computing hash for provider (12/22) v Computing hash for drug_era (13/22) [59ms] i Computing hash for drug_era (13/22) v Computing hash for dose_era (14/22) [53ms] i Computing hash for dose_era (14/22) v Computing hash for condition_era (15/22) [60ms] i Computing hash for condition_era (15/22) v Computing hash for concept (16/22) [53ms] i Computing hash for concept (16/22) v Computing hash for vocabulary (17/22) [58ms] i Computing hash for vocabulary (17/22) v Computing hash for concept_relationship (18/22) [48ms] i Computing hash for concept_relationship (18/22) v Computing hash for concept_ancestor (19/22) [48ms] i Computing hash for concept_ancestor (19/22) v Computing hash for concept_synonym (20/22) [53ms] i Computing hash for concept_synonym (20/22) v Computing hash for drug_strength (21/22) [55ms] i Computing hash for drug_strength (21/22) v Computing hash for cdm_source (22/22) [44ms] i Computing hash for cdm_source (22/22) * Computing CDM table hashes took 1.29 secs v Computing hash for cdm_source (22/22) [74ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_male v Generating cohort (1/1) - gibleed_male [518ms] Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable', target signature 'duckdb_connection#Id'. "duckdb_connection#ANY" would also be valid [ FAIL 0 | WARN 0 | SKIP 21 | PASS 371 ] ══ Skipped tests (21) ══════════════════════════════════════════════════════════ • "postgres" %in% dbToTest is not TRUE (1): 'test-02-db-cdm.R:299:3' • On CRAN (8): 'test-04-db-generateConceptCohortSet.R:399:3', 'test-04-db-generateConceptCohortSet.R:417:3', 'test-04-db-generateConceptCohortSet.R:443:3', 'test-Eunomia.R:61:3', 'test-db-recordCohortAttrition.R:121:5', 'test-db-recordCohortAttrition.R:134:3', 'test-memory-issue.R:6:3', 'test-write_prefix_cohort_generation_snowflake.R:4:3' • eunomiaIsAvailable("empty_cdm") is not TRUE (1): 'test-Eunomia.R:42:3' • failing test (2): 'test-07-db-dateadd.R:126:3', 'test-db-in_schema.R:34:5' • manual test (7): 'test-02-db-cdm.R:240:3', 'test-03-db-generateCohortSet.R:115:3', 'test-03-db-generateCohortSet.R:256:3', 'test-09-db-copy_cdm_to.R:62:3', 'test-Eunomia.R:2:3', 'test-db-in_schema.R:46:3', 'test-db-write_schema_with_database.R:5:3' • {Capr} is not installed (1): 'test-04-db-generateConceptCohortSet.R:597:3' • {TreatmentPatterns} is not installed (1): 'test-03-db-generateCohortSet.R:134:3' [ FAIL 0 | WARN 0 | SKIP 21 | PASS 371 ] > > > > > > proc.time() user system elapsed 297.29 49.46 268.68