Running ‘testthat.R’ [189s/254s]
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/RtmpqF9zpC/file38f4a85be1b164/GiBleed_5.3.zip
  Creating a new cdm
  Uploading table person (1 rows) - [1/3]
  Uploading table observation_period (1 rows) - [2/3]
  Uploading table vocabulary (125 rows) - [3/3]
  Creating a new cdm
  Uploading table person (1 rows) - [1/3]
  Creating a new cdm
  Uploading table person (2694 rows) - [1/35]
  Uploading table observation_period (5343 rows) - [2/35]
  Uploading table visit_occurrence (1037 rows) - [3/35]
  Uploading table visit_detail (0 rows) - [4/35]
  Uploading table condition_occurrence (65332 rows) - [5/35]
  Uploading table drug_exposure (67707 rows) - [6/35]
  Uploading table procedure_occurrence (37409 rows) - [7/35]
  Uploading table device_exposure (0 rows) - [8/35]
  Uploading table measurement (44053 rows) - [9/35]
  Uploading table observation (1477 rows) - [10/35]
  Uploading table death (0 rows) - [11/35]
  Uploading table note (0 rows) - [12/35]
  Uploading table note_nlp (0 rows) - [13/35]
  Uploading table specimen (0 rows) - [14/35]
  Uploading table fact_relationship (0 rows) - [15/35]
  Uploading table location (0 rows) - [16/35]
  Uploading table care_site (0 rows) - [17/35]
  Uploading table provider (0 rows) - [18/35]
  Uploading table payer_plan_period (0 rows) - [19/35]
  Uploading table cost (0 rows) - [20/35]
  Uploading table drug_era (52508 rows) - [21/35]
  Uploading table dose_era (0 rows) - [22/35]
  Uploading table condition_era (65719 rows) - [23/35]
  Uploading table metadata (0 rows) - [24/35]
  Uploading table cdm_source (1 rows) - [25/35]
  Uploading table concept (444 rows) - [26/35]
  Uploading table vocabulary (125 rows) - [27/35]
  Uploading table domain (45 rows) - [28/35]
  Uploading table concept_class (0 rows) - [29/35]
  Uploading table concept_relationship (8 rows) - [30/35]
  Uploading table relationship (480 rows) - [31/35]
  Uploading table concept_synonym (1064 rows) - [32/35]
  Uploading table concept_ancestor (65690 rows) - [33/35]
  Uploading table source_to_concept_map (0 rows) - [34/35]
  Uploading table drug_strength (0 rows) - [35/35]
  Creating a new cdm
  Uploading table person (2694 rows) - [1/35]
  Uploading table observation_period (5343 rows) - [2/35]
  Uploading table visit_occurrence (1037 rows) - [3/35]
  Uploading table visit_detail (0 rows) - [4/35]
  Uploading table condition_occurrence (65332 rows) - [5/35]
  Uploading table drug_exposure (67707 rows) - [6/35]
  Uploading table procedure_occurrence (37409 rows) - [7/35]
  Uploading table device_exposure (0 rows) - [8/35]
  Uploading table measurement (44053 rows) - [9/35]
  Uploading table observation (1477 rows) - [10/35]
  Uploading table death (0 rows) - [11/35]
  Uploading table note (0 rows) - [12/35]
  Uploading table note_nlp (0 rows) - [13/35]
  Uploading table specimen (0 rows) - [14/35]
  Uploading table fact_relationship (0 rows) - [15/35]
  Uploading table location (0 rows) - [16/35]
  Uploading table care_site (0 rows) - [17/35]
  Uploading table provider (0 rows) - [18/35]
  Uploading table payer_plan_period (0 rows) - [19/35]
  Uploading table cost (0 rows) - [20/35]
  Uploading table drug_era (52508 rows) - [21/35]
  Uploading table dose_era (0 rows) - [22/35]
  Uploading table condition_era (65719 rows) - [23/35]
  Uploading table metadata (0 rows) - [24/35]
  Uploading table cdm_source (1 rows) - [25/35]
  Uploading table concept (444 rows) - [26/35]
  Uploading table vocabulary (125 rows) - [27/35]
  Uploading table domain (45 rows) - [28/35]
  Uploading table concept_class (0 rows) - [29/35]
  Uploading table concept_relationship (8 rows) - [30/35]
  Uploading table relationship (480 rows) - [31/35]
  Uploading table concept_synonym (1064 rows) - [32/35]
  Uploading table concept_ancestor (65690 rows) - [33/35]
  Uploading table source_to_concept_map (0 rows) - [34/35]
  Uploading table drug_strength (0 rows) - [35/35]
  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/RtmpqF9zpC'.
  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/RtmpqF9zpC/GiBleed_5.3.zip
  Found 420 distinct concept_ids in clinical tables.
  After adding ancestors: 39367 concept_ids.
  Your SQL query is over 20,000 characters which can cause issues on some database platforms!
  Try calling computeQuery earlier in your pipeline.
  Your SQL query is over 20,000 characters which can cause issues on some database platforms!
  Try calling computeQuery earlier in your pipeline.
  Vocabulary trimming complete.
  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
  Creating a new cdm
  Uploading table person (2694 rows) - [1/2]
  Uploading table observation_period (5343 rows) - [2/2]
  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 2 | WARN 0 | SKIP 56 | PASS 286 ]
  
  ══ Skipped tests (56) ══════════════════════════════════════════════════════════
  • "snowflake" %in% dbToTest is not TRUE (1): 'test-cdmDisconnect.R:5:3'
  • On CRAN (30): 'test-04-db-generateConceptCohortSet.R:399:3',
    'test-04-db-generateConceptCohortSet.R:415:3',
    'test-04-db-generateConceptCohortSet.R:439:3',
    'test-04-db-generateConceptCohortSet.R:507:3',
    'test-04-db-generateConceptCohortSet.R:568:3',
    'test-04-db-generateConceptCohortSet.R:616:3', 'test-07-db-dateadd.R:327:3',
    'test-16-db-dbSource.R:85:3', 'test-Eunomia.R:41:3', 'test-Eunomia.R:63:3',
    'test-buildEraTables.R:4:1', 'test-cdm-extra.R:5:1',
    'test-cdmDisconnect.R:59:3', 'test-cdmFromCohortSet-extra.R:4:1',
    'test-cdmFromCohortSet.R:2:1', 'test-cohdSimilarConcepts.R:2:1',
    'test-cohort-reconnect.R:5:1', 'test-compute-extra.R:4:1',
    'test-copyCdmTo-extra.R:4:1', 'test-dateadd-extra.R:4:1',
    'test-db-recordCohortAttrition.R:121:5',
    'test-db-recordCohortAttrition.R:134:3', 'test-dbSource-extra.R:4:1',
    'test-generateCohortSet-extra.R:5:1',
    'test-generateConceptCohortSet-extra.R:4:1',
    'test-local-generateCohortSet.R:8:3', 'test-memory-issue.R:6:3',
    'test-misc-extra.R:4:1', 'test-summariseQuantile-extra.R:4:1',
    'test-utils-extra.R:4:1'
  • dateadd requires magrittr pipe (%>%); direct mutate() and native pipe (|>)
    not supported (1): 'test-07-db-dateadd.R:126:3'
  • failing test (1): 'test-db-in_schema.R:34:5'
  • manual test (7): 'test-02-db-cdm.R:237:3',
    'test-03-db-generateCohortSet.R:115:3',
    'test-03-db-generateCohortSet.R:256:3', 'test-09-db-copy_cdm_to.R:60:3',
    '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:593:3'
  • {CirceR} is not installed (10): 'test-03-db-generateCohortSet.R:69:5',
    'test-03-db-generateCohortSet.R:219:3',
    'test-03-db-generateCohortSet.R:278:3',
    'test-03-db-generateCohortSet.R:296:3',
    '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:124:3',
    'test-18-db-newGeneratedCohortSet.R:177:3',
    'test-write_prefix_cohort_generation_snowflake.R:3:3'
  • {DatabaseConnector} is not installed (3): 'test-02-db-cdm.R:269:3',
    'test-02-db-cdm.R:295:3', 'test-02-db-cdm.R:328:3'
  • {SqlRender} is not installed. (1): 'test-db-utils.R:190:7'
  • {TreatmentPatterns} is not installed (1):
    'test-03-db-generateCohortSet.R:139:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── 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 2 | WARN 0 | SKIP 56 | PASS 286 ]
  Error:
  ! Test failures.
  Execution halted