Package: CDMConnector [Old version: 2.1.1, New version: 2.2.0] Check: tests New result: ERROR Running ‘testthat.R’ [282s/364s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # 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 /home/hornik/tmp/scratch/Rtmp5rQrPx/file3eb7c77c909f41/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 [812ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [247ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [260ms] i Generating 3 cohorts i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [877ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [214ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [224ms] 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 [297ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [280ms] i Generating 1 cohort i Generating cohort (1/1) - deep_vein_thrombosis_01 v Generating cohort (1/1) - deep_vein_thrombosis_01 [223ms] i Generating 1 cohort i Generating cohort (1/1) - deep_vein_thrombosis_01 v Generating cohort (1/1) - deep_vein_thrombosis_01 [269ms] 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 [653ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_default v Generating cohort (1/1) - gibleed_default [540ms] i Generating 1 cohort i Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (1/1) - cerebral_venous_sinus_thrombosis_01 [164ms] i Generating 5 cohorts i Generating cohort (1/5) - gibleed_all v Generating cohort (1/5) - gibleed_all [296ms] i Generating cohort (2/5) - gibleed_default v Generating cohort (2/5) - gibleed_default [237ms] i Generating cohort (3/5) - gibleed_default_with_descendants v Generating cohort (3/5) - gibleed_default_with_descendants [210ms] i Generating cohort (4/5) - gibleed_all_end_10 v Generating cohort (4/5) - gibleed_all_end_10 [4.1s] i Generating cohort (5/5) - gibleed_end_10 v Generating cohort (5/5) - gibleed_end_10 [1.1s] 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 [234ms] i Generating cohort (2/2) - deep_vein_thrombosis_01 v Generating cohort (2/2) - deep_vein_thrombosis_01 [189ms] i Generating 3 cohorts i Generating cohort (1/3) - another_gibleed_male v Generating cohort (1/3) - another_gibleed_male [654ms] i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01 [167ms] i Generating cohort (3/3) - another_deep_vein_thrombosis_01 v Generating cohort (3/3) - another_deep_vein_thrombosis_01 [172ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [747ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [159ms] i Generating cohort (3/3) - deep_vein_thrombosis_01 v Generating cohort (3/3) - deep_vein_thrombosis_01 [162ms] i Generating 3 cohorts i Generating cohort (1/3) - gibleed_male v Generating cohort (1/3) - gibleed_male [816ms] i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01 [240ms] 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: '/home/hornik/tmp/scratch/Rtmp5rQrPx'. 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 /home/hornik/tmp/scratch/Rtmp5rQrPx/GiBleed_5.3.zip =================>------------- 56% | ETA: 2s 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 [309ms] i Generating 1 cohort i Generating cohort (1/1) - gibleed_male v Generating cohort (1/1) - gibleed_male [612ms] 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 0 | SKIP 22 | PASS 348 ] ══ Skipped tests (22) ══════════════════════════════════════════════════════════ • "postgres" %in% dbToTest is not TRUE (1): 'test-02-db-cdm.R:299:3' • Installed DatabaseConnector is version 6.4.0; but 7.0.0 is required (1): 'test-db-utils.R:258:5' • 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' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-04-db-generateConceptCohortSet.R:392:5'): duckdb - generateConceptCohortSet ── Error in `map(.x, .f, ..., .progress = .progress)`: i In index: 1. i With name: gibleed. Caused by error in `.f()`: ! Assertion on '.' failed: Must be of type 'integerish', not 'tbl_df/tbl/data.frame'. Backtrace: ▆ 1. ├─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-04-db-generateConceptCohortSet.R:392:5 2. │ └─CDMConnector::generateConceptCohortSet(...) at test-04-db-generateConceptCohortSet.R:171:3 3. │ └─purrr::walk(...) 4. │ └─purrr::map(.x, .f, ..., .progress = .progress) 5. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 6. │ ├─purrr:::with_indexed_errors(...) 7. │ │ └─base::withCallingHandlers(...) 8. │ ├─purrr:::call_with_cleanup(...) 9. │ └─CDMConnector (local) .f(.x[[i]], ...) 10. │ └─checkmate::assert_integerish(., lower = 0, min.len = 1, any.missing = FALSE) 11. │ └─checkmate::makeAssertion(x, res, .var.name, add) 12. │ └─checkmate:::mstop(...) 13. │ └─base::stop(simpleError(sprintf(msg, ...), call.)) 14. └─purrr (local) ``(``) 15. └─cli::cli_abort(...) 16. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 22 | PASS 348 ] Error: Test failures Execution halted