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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\2024_11_12_17_00_02_27104\RtmpWK3GpH\file17f14404d4689/GiBleed_5.3.zip Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable', target signature 'duckdb_connection#Id'. "duckdb_connection#ANY" would also be valid Support for 'prefix' in write_schema is deprecated and will be removed in a future release. Please use the `writePrefix` argument in `cdmFromCon()` instead. This message is displayed once per session. i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [887ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [255ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [237ms] i Generating 3 cohorts i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [718ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [248ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [226ms] 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 [227ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [235ms] i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [222ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [217ms] i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [229ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [279ms] i Generating 2 cohorts i Generating 2 cohorts i Generating 2 cohorts i Generating 1 cohort i Generating cohort (1/1) - gibleed_default v Generating cohort (1/1) - gibleed_default [343ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_default_with_descendants v Generating cohort (1/1) - gibleed_default_with_descendants [493ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_all v Generating cohort (1/1) - gibleed_all [269ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_all v Generating cohort (1/1) - gibleed_all [332ms] i Generating 1 cohort i Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 [239ms] Attaching package: 'clock' The following object is masked from 'package:CDMConnector': as_date i Generating 5 cohorts i Generating cohort (1/5) - gibleed_all v Generating cohort (1/5) - gibleed_all [301ms] i Generating cohort (2/5) - gibleed_default v Generating cohort (2/5) - gibleed_default [342ms] i Generating cohort (3/5) - gibleed_default_with_descendants v Generating cohort (3/5) - gibleed_default_with_descendants [320ms] i Generating cohort (4/5) - gibleed_all_end_10 v Generating cohort (4/5) - gibleed_all_end_10 [375ms] i Generating cohort (5/5) - gibleed_end_10 v Generating cohort (5/5) - gibleed_end_10 [370ms] Getting distinct count of concept relationship table 0.1 sec elapsed Getting count of different relationship IDs in concept relationship table 0.09 sec elapsed Getting join of concept and concept class computed to a temp table 0.13 sec elapsed Getting concept table collected into memory 0 sec elapsed Getting join of person and observation period collected into memory 0.07 sec elapsed Getting summary of observation period start and end dates by gender concept id 0.15 sec elapsed i Generating 2 cohorts i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01 [235ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [261ms] i Generating 3 cohorts i Generating cohort (1/3) - another_gibleed_male v Generating cohort (1/3) - another_gibleed_male [599ms] i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 [205ms] i Generating cohort (3/3) - another_deep_vein_thrombosis_01 v Generating cohort (3/3) - another_deep_vein_thrombosis_01 [264ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [604ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [199ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [259ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [612ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [251ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [217ms] i `EUNOMIA_DATA_FOLDER` set to: 'D:\temp\2024_11_12_17_00_02_27104\RtmpWK3GpH'. 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\2024_11_12_17_00_02_27104\RtmpWK3GpH/GiBleed_5.3.zip Getting distinct count of concept relationship table 0.08 sec elapsed Getting count of different relationship IDs in concept relationship table 0.06 sec elapsed Getting join of concept and concept class computed to a temp table 0.09 sec elapsed Getting concept table collected into memory 0 sec elapsed Getting join of person and observation period collected into memory 0.06 sec elapsed Getting summary of observation period start and end dates by gender concept id 0.14 sec elapsed 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 22 | PASS 327 ] ══ Skipped tests (22) ══════════════════════════════════════════════════════════ • On CRAN (8): 'test-04-db-generateConceptCohortSet.R:381:3', 'test-04-db-generateConceptCohortSet.R:399:3', 'test-04-db-generateConceptCohortSet.R:425:3', 'test-Eunomia.R:59:3', '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' • arrow::write_parquet is failing (1): 'test-local_cdm.R:3:3' • empty test (2): 'test-03-db-generateCohortSet.R:214:1', 'test-06-db-compute.R:91:1' • eunomia_is_available("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:27:5' • manual test (6): 'test-02-db-cdm.R:235:3', 'test-03-db-generateCohortSet.R:111:3', 'test-03-db-generateCohortSet.R:248:3', 'test-09-db-copy_cdm_to.R:62:3', 'test-Eunomia.R:2:3', 'test-db-write_schema_with_database.R:5:3' • {Capr} is not installed (1): 'test-04-db-generateConceptCohortSet.R:578:3' • {TreatmentPatterns} is not installed (1): 'test-03-db-generateCohortSet.R:130:3' [ FAIL 0 | WARN 0 | SKIP 22 | PASS 327 ] > > > > > > proc.time() user system elapsed 327.73 45.26 309.06