Running ‘testthat.R’ [284s/276s]
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://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 /tmp/Rtmpo0Da3I/working_dir/Rtmp19R0zo/file3031ae1bf81ec3/GiBleed_5.3.zip
  ====================>----------   67% | ETA:  1s
  i Generating 5 cohorts
  i Generating cohort (1/5) - gibleed_all)
  v Generating cohort (1/5) - gibleed_all) [761ms]
  
  i Generating cohort (2/5) - gibleed_all_end_10)
  v Generating cohort (2/5) - gibleed_all_end_10) [513ms]
  
  i Generating cohort (3/5) - gibleed_default)
  v Generating cohort (3/5) - gibleed_default) [335ms]
  
  i Generating cohort (4/5) - gibleed_default_with_descendants)
  v Generating cohort (4/5) - gibleed_default_with_descendants) [340ms]
  
  i Generating cohort (5/5) - gibleed_end_10)
  v Generating cohort (5/5) - gibleed_end_10) [359ms]
  
  i Generating 3 cohorts
  i Generating cohort (1/3) - gibleed_male)
  v Generating cohort (1/3) - gibleed_male) [822ms]
  
  i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [230ms]
  
  i Generating cohort (3/3) - deep_vein_thrombosis_01)
  v Generating cohort (3/3) - deep_vein_thrombosis_01) [256ms]
  
  i Generating 3 cohorts
  i Generating 3 cohorts
  i Generating cohort (1/3) - gibleed_male)
  v Generating cohort (1/3) - gibleed_male) [743ms]
  
  i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [257ms]
  
  i Generating cohort (3/3) - deep_vein_thrombosis_01)
  v Generating cohort (3/3) - deep_vein_thrombosis_01) [273ms]
  
  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) [253ms]
  
  i Generating cohort (2/2) - deep_vein_thrombosis_01)
  v Generating cohort (2/2) - deep_vein_thrombosis_01) [334ms]
  
  i Generating 2 cohorts
  i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) [231ms]
  
  i Generating cohort (2/2) - deep_vein_thrombosis_01)
  v Generating cohort (2/2) - deep_vein_thrombosis_01) [215ms]
  
  i Generating 2 cohorts
  i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) [208ms]
  
  i Generating cohort (2/2) - deep_vein_thrombosis_01)
  v Generating cohort (2/2) - deep_vein_thrombosis_01) [264ms]
  
  i Generating 2 cohorts
  i Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (1/2) - cerebral_venous_sinus_thrombosis_01) [267ms]
  
  i Generating cohort (2/2) - deep_vein_thrombosis_01)
  v Generating cohort (2/2) - deep_vein_thrombosis_01) [287ms]
  
  i Generating 3 cohorts
  i Generating cohort (1/3) - another_gibleed_male)
  v Generating cohort (1/3) - another_gibleed_male) [916ms]
  
  i Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (2/3) - another_cerebral_venous_sinus_thrombosis_01) [319ms]
  
  i Generating cohort (3/3) - another_deep_vein_thrombosis_01)
  v Generating cohort (3/3) - another_deep_vein_thrombosis_01) [308ms]
  
  i Generating 3 cohorts
  i Generating cohort (1/3) - gibleed_male)
  v Generating cohort (1/3) - gibleed_male) [635ms]
  
  i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [249ms]
  
  i Generating cohort (3/3) - deep_vein_thrombosis_01)
  v Generating cohort (3/3) - deep_vein_thrombosis_01) [286ms]
  
  i Generating 3 cohorts
  i Generating cohort (1/3) - gibleed_male)
  v Generating cohort (1/3) - gibleed_male) [571ms]
  
  i Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01)
  v Generating cohort (2/3) - cerebral_venous_sinus_thrombosis_01) [232ms]
  
  i Generating cohort (3/3) - deep_vein_thrombosis_01)
  v Generating cohort (3/3) - deep_vein_thrombosis_01) [270ms]
  
  [ FAIL 1 | WARN 0 | SKIP 17 | PASS 260 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • Capr cannot be loaded (1): 'test-db-generateCohortSet.R:77:3'
  • On CRAN (9): 'test-db-generateCohortSet.R:128:3',
    'test-db-generateConceptCohortSet.R:315:3',
    'test-db-generateConceptCohortSet.R:332:3',
    'test-db-generateConceptCohortSet.R:357:3',
    'test-db-recordCohortAttrition.R:121:5',
    'test-db-recordCohortAttrition.R:134:3', 'test-local_cdm.R:5:3',
    'test-memory-issue.R:6:3',
    'test-write_prefix_cohort_generation_snowflake.R:4:3'
  • eunomia_is_available("empty_cdm") is not TRUE (1): 'test-Eunomia.R:42:3'
  • failing test (1): 'test-db-dateadd.R:126:3'
  • manual test (5): 'test-Eunomia.R:2:3', 'test-db-copy_cdm_to.R:62:3',
    'test-db-generateCohortSet.R:108:3', 'test-db-generateCohortSet.R:243:3',
    'test-db-write_schema_with_database.R:5:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-db-generateConceptCohortSet.R:308:5'): duckdb - generateConceptCohortSet ──
  Error in `.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)`: invalid non-character version specification 'x' (type: double)
  Backtrace:
      ▆
   1. └─CDMConnector (local) test_generate_concept_cohort_set(con, cdm_schema, write_schema) at test-db-generateConceptCohortSet.R:308:5
   2.   └─CDMConnector::generateConceptCohortSet(...) at test-db-generateConceptCohortSet.R:18:3
   3.     └─base::Ops.numeric_version(...)
   4.       └─base::as.numeric_version(e2)
   5.         └─base::numeric_version(x)
   6.           └─base::.make_numeric_version(x, strict, .standard_regexps()$valid_numeric_version)
  
  [ FAIL 1 | WARN 0 | SKIP 17 | PASS 260 ]
  Error: Test failures
  In addition: Warning message:
  Connection is garbage-collected, use dbDisconnect() to avoid this. 
  Execution halted