Running ‘testthat.R’ [189s/255s]
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 /tmp/RtmpGjAiBA/file30ad6f4f9556ac/GiBleed_5.3.zip
  Saving _problems/test-04-db-generateConceptCohortSet-584.R
  ========================>------   79% | ETA:  1s
  ===========>-------------------   36% | ETA:  4s
  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 `EUNOMIA_DATA_FOLDER` set to: '/tmp/RtmpGjAiBA'.
  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 /tmp/RtmpGjAiBA/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
  Saving _problems/test-db-cdmSubset-112.R
  Saving _problems/test-omopgenerics-16.R
  Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
   target signature 'duckdb_connection#Id'.
   "duckdb_connection#ANY" would also be valid
  [ FAIL 3 | WARN 0 | SKIP 33 | PASS 264 ]
  
  ══ Skipped tests (33) ══════════════════════════════════════════════════════════
  • On CRAN (7): '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'
  • 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'
  • {CirceR} is not installed (10): 'test-03-db-generateCohortSet.R:69:5',
    'test-03-db-generateCohortSet.R:217:3',
    'test-03-db-generateCohortSet.R:278:3',
    'test-03-db-generateCohortSet.R:297:3',
    'test-04-db-generateConceptCohortSet.R:387:5',
    'test-13-db-custom_cohort_creation.R:35:5', 'test-17-db-generic-bind.R:22:5',
    'test-18-db-newGeneratedCohortSet.R:126:3',
    'test-18-db-newGeneratedCohortSet.R:181:3',
    'test-write_prefix_cohort_generation_snowflake.R:3:3'
  • {DatabaseConnector} is not installed (3): 'test-02-db-cdm.R:271:3',
    'test-02-db-cdm.R:297:3', 'test-db-utils.R:258:5'
  • {SqlRender} is not installed. (1): 'test-db-utils.R:194:7'
  • {TreatmentPatterns} is not installed (1):
    'test-03-db-generateCohortSet.R:134:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-04-db-generateConceptCohortSet.R:582:3'): attrition columns are correct ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `generateCohortSet(cdm, cohortSet = cohort_set, name = "cohort2")`: The package "CirceR" is required.
  Backtrace:
      ▆
   1. └─CDMConnector::generateCohortSet(...) at test-04-db-generateConceptCohortSet.R:582:3
   2.   └─rlang::check_installed("CirceR")
  ── Error ('test-db-cdmSubset.R:112:5'): duckdb - sample database ───────────────
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `generateCohortSet(cdm, cohortSet = cohortSet, name = "cohort")`: The package "CirceR" is required.
  Backtrace:
      ▆
   1. └─CDMConnector (local) test_cdmSubset(con, cdmSchema, writeSchema) at test-db-cdmSubset.R:112:5
   2.   └─CDMConnector::generateCohortSet(cdm, cohortSet = cohortSet, name = "cohort") at test-db-cdmSubset.R:13:3
   3.     └─rlang::check_installed("CirceR")
  ── Error ('test-omopgenerics.R:13:3'): omopgenerics::bind works for combining cohort tables ──
  <rlib_error_package_not_found/rlang_error/error/condition>
  Error in `CDMConnector::generateCohortSet(cdm, cohortSet, name = "cohort1", overwrite = TRUE)`: The package "CirceR" is required.
  Backtrace:
      ▆
   1. └─CDMConnector::generateCohortSet(...) at test-omopgenerics.R:13:3
   2.   └─rlang::check_installed("CirceR")
  
  [ FAIL 3 | WARN 0 | SKIP 33 | PASS 264 ]
  Error:
  ! Test failures.
  Execution halted