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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://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Download completed! Creating CDM database D:\temp\2025_02_20_18_25_17_12396\RtmpCG9bPw\file18b983f655ac7/GiBleed_5.3.zip i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [600ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [152ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [167ms] i Generating 3 cohorts i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [459ms] 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 [154ms] 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 [147ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [155ms] i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [157ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [152ms] i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [143ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [141ms] 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 [464ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_default v Generating cohort (1/1) - gibleed_default [262ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_default_with_descendants v Generating cohort (1/1) - gibleed_default_with_descendants [279ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_all v Generating cohort (1/1) - gibleed_all [272ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_all v Generating cohort (1/1) - gibleed_all [270ms] i Generating 1 cohort i Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 [139ms] i Generating 5 cohorts i Generating cohort (1/5) - gibleed_all v Generating cohort (1/5) - gibleed_all [274ms] i Generating cohort (2/5) - gibleed_default v Generating cohort (2/5) - gibleed_default [279ms] i Generating cohort (3/5) - gibleed_default_with_descendants v Generating cohort (3/5) - gibleed_default_with_descendants [283ms] i Generating cohort (4/5) - gibleed_all_end_10 v Generating cohort (4/5) - gibleed_all_end_10 [296ms] i Generating cohort (5/5) - gibleed_end_10 v Generating cohort (5/5) - gibleed_end_10 [284ms] 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 [138ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [135ms] i Generating 3 cohorts i Generating cohort (1/3) - another_gibleed_male v Generating cohort (1/3) - another_gibleed_male [461ms] i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 [136ms] i Generating cohort (3/3) - another_deep_vein_thrombosis_01 v Generating cohort (3/3) - another_deep_vein_thrombosis_01 [141ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [467ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [131ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [139ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [428ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [139ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [140ms] i `EUNOMIA_DATA_FOLDER` set to: 'D:\temp\2025_02_20_18_25_17_12396\RtmpCG9bPw'. trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Download completed! Creating CDM database D:\temp\2025_02_20_18_25_17_12396\RtmpCG9bPw/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 [496ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_male v Generating cohort (1/1) - gibleed_male [449ms] Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable', target signature 'duckdb_connection#Id'. "duckdb_connection#ANY" would also be valid [ FAIL 1 | WARN 1 | SKIP 20 | PASS 364 ] ══ Skipped tests (20) ══════════════════════════════════════════════════════════ • On CRAN (8): 'test-04-db-generateConceptCohortSet.R:384:3', 'test-04-db-generateConceptCohortSet.R:402:3', 'test-04-db-generateConceptCohortSet.R:428:3', '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:233:3', 'test-03-db-generateCohortSet.R:109:3', 'test-03-db-generateCohortSet.R:244:3', '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:582:3' • {TreatmentPatterns} is not installed (1): 'test-03-db-generateCohortSet.R:128:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-07-db-dateadd.R:263:5'): duckdb - date functions ─────────────── Error in `abs(df$dif_days)`: non-numeric argument to mathematical function Backtrace: ▆ 1. └─CDMConnector (local) test_clock_functions(con, write_schema) at test-07-db-dateadd.R:263:5 [ FAIL 1 | WARN 1 | SKIP 20 | PASS 364 ] Error: Test failures Execution halted