Running ‘testthat.R’ [219s/278s]
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://raw.githubusercontent.com/darwin-eu/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip'
  Content type 'application/zip' length 6848518 bytes (6.5 MB)
  ==================================================
  downloaded 6.5 MB
  
  Dataset already exists (/tmp/Rtmp0htiC3/file11c3d62492503/GiBleed_5.3.zip). Specify overwrite=T to overwrite existing zip archive.attempting to extract and load /tmp/Rtmp0htiC3/file11c3d62492503/GiBleed_5.3.zip
  [ FAIL 14 | WARN 0 | SKIP 50 | PASS 286 ]
  
  ══ Skipped tests (50) ══════════════════════════════════════════════════════════
  • Capr cannot be loaded (1): 'test-generateCohortSet.R:391:3'
  • CirceR cannot be loaded (5): 'test-generateCohortSet.R:5:3',
    'test-generateCohortSet.R:73:3', 'test-generateCohortSet.R:146:3',
    'test-generateCohortSet.R:208:3', 'test-generateCohortSet.R:267:3'
  • On CRAN (4): 'test-cdm.R:246:3', 'test-cdmSubset.R:271:3',
    'test-summarise_quantile.R:501:3', 'test-zzz-dplyr.R:156:3'
  • Sys.getenv("BIGQUERY_SERVICE_ACCOUNT_JSON_PATH") == "" is TRUE (1):
    'test-intersect.R:227:3'
  • Sys.getenv("CDM5_POSTGRESQL_USER") == "" is TRUE (10): 'test-cdm.R:42:3',
    'test-cdm.R:493:3', 'test-cdmSubset.R:104:3', 'test-compute.R:35:3',
    'test-compute.R:448:3', 'test-dateadd.R:66:3', 'test-intersect.R:158:3',
    'test-summarise_quantile.R:271:3', 'test-summarise_quantile.R:396:3',
    'test-zzz-dplyr.R:51:3'
  • Sys.getenv("CDM5_REDSHIFT_USER") == "" is TRUE (9): 'test-cdm.R:174:3',
    'test-cdm.R:523:3', 'test-cdmSubset.R:217:3', 'test-compute.R:146:3',
    'test-dateadd.R:187:3', 'test-intersect.R:212:3',
    'test-summarise_quantile.R:352:3', 'test-summarise_quantile.R:467:3',
    'test-zzz-dplyr.R:122:3'
  • Sys.getenv("CDM5_SQL_SERVER_USER") == "" is TRUE (11): 'test-cdm.R:74:3',
    'test-cdm.R:553:3', 'test-cdmSubset.R:155:3', 'test-compute.R:87:3',
    'test-compute.R:481:3', 'test-dateadd.R:123:3', 'test-intersect.R:172:3',
    'test-intersect.R:188:3', 'test-summarise_quantile.R:310:3',
    'test-summarise_quantile.R:431:3', 'test-zzz-dplyr.R:86:3'
  • Sys.getenv("LOCAL_POSTGRESQL_USER") == "" is TRUE (4): 'test-cdm.R:7:3',
    'test-cdm.R:464:3', 'test-cdmSubset.R:53:3', 'test-intersect.R:145:3'
  • Sys.getenv("REDSHIFT_USER") == "" is TRUE (1): 'test-zzz-DBI.R:4:3'
  • Sys.getenv("SNOWFLAKE_USER") == "" is TRUE (1): 'test-cdm.R:586:3'
  • failing test (1): 'test-cdm.R:293:3'
  • manual test (2): 'test-summarise_quantile.R:560:3', 'test-zzz-dplyr.R:216:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-cdm.R:212:3'): spark cdm_reference ─────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'odbc'
  Backtrace:
      ▆
   1. ├─testthat::skip_if_not("Databricks" %in% odbc::odbcListDataSources()$name) at test-cdm.R:212:2
   2. │ └─base::isTRUE(condition)
   3. ├─"Databricks" %in% odbc::odbcListDataSources()$name
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-cdmSubset.R:322:3'): spark subsetting ──────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'odbc'
  Backtrace:
      ▆
   1. ├─testthat::skip_if_not("Databricks" %in% odbc::odbcListDataSources()$name) at test-cdmSubset.R:322:2
   2. │ └─base::isTRUE(condition)
   3. ├─"Databricks" %in% odbc::odbcListDataSources()$name
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-cdmSubset.R:369:3'): snowflake subsetting ──────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'odbc'
  Backtrace:
      ▆
   1. ├─testthat::skip_if_not("Snowflake" %in% odbc::odbcListDataSources()$name) at test-cdmSubset.R:369:2
   2. │ └─base::isTRUE(condition)
   3. ├─"Snowflake" %in% odbc::odbcListDataSources()$name
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-compute.R:206:3'): computeQuery works on Snowflake ─────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'odbc'
  Backtrace:
      ▆
   1. ├─testthat::skip_if_not("Snowflake" %in% odbc::odbcListDataSources()$name) at test-compute.R:206:2
   2. │ └─base::isTRUE(condition)
   3. ├─"Snowflake" %in% odbc::odbcListDataSources()$name
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-compute.R:268:3'): computeQuery works on Spark ─────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'odbc'
  Backtrace:
      ▆
   1. ├─testthat::skip_if_not("Databricks" %in% odbc::odbcListDataSources()$name) at test-compute.R:268:2
   2. │ └─base::isTRUE(condition)
   3. ├─"Databricks" %in% odbc::odbcListDataSources()$name
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-compute.R:336:3'): computeQuery works on Oracle ────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'odbc'
  Backtrace:
      ▆
   1. ├─testthat::skip_if_not("OracleODBC-19" %in% odbc::odbcListDataSources()$name) at test-compute.R:336:2
   2. │ └─base::isTRUE(condition)
   3. ├─"OracleODBC-19" %in% odbc::odbcListDataSources()$name
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-dateadd.R:249:3'): Date functions work on Spark ────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'odbc'
  Backtrace:
      ▆
   1. ├─testthat::skip_if_not("Databricks" %in% odbc::odbcListDataSources()$name) at test-dateadd.R:249:2
   2. │ └─base::isTRUE(condition)
   3. ├─"Databricks" %in% odbc::odbcListDataSources()$name
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-dateadd.R:310:3'): Date functions work on Oracle ───────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'odbc'
  Backtrace:
      ▆
   1. ├─testthat::skip_if_not("OracleODBC-19" %in% odbc::odbcListDataSources()$name) at test-dateadd.R:310:2
   2. │ └─base::isTRUE(condition)
   3. ├─"OracleODBC-19" %in% odbc::odbcListDataSources()$name
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-generateCohortSet.R:327:3'): cohort generation works on spark ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'odbc'
  Backtrace:
      ▆
   1. ├─testthat::skip_if_not("Databricks" %in% odbc::odbcListDataSources()$name) at test-generateCohortSet.R:327:2
   2. │ └─base::isTRUE(condition)
   3. ├─"Databricks" %in% odbc::odbcListDataSources()$name
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-intersect.R:203:3'): intersect - oracle ────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'odbc'
  Backtrace:
      ▆
   1. ├─testthat::skip_if_not("OracleODBC-19" %in% odbc::odbcListDataSources()$name) at test-intersect.R:203:2
   2. │ └─base::isTRUE(condition)
   3. ├─"OracleODBC-19" %in% odbc::odbcListDataSources()$name
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-summarise_quantile.R:530:3'): quantile translation works on Spark ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'odbc'
  Backtrace:
      ▆
   1. ├─testthat::skip_if_not("Databricks" %in% odbc::odbcListDataSources()$name) at test-summarise_quantile.R:530:2
   2. │ └─base::isTRUE(condition)
   3. ├─"Databricks" %in% odbc::odbcListDataSources()$name
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-zzz-dplyr.R:2:3'): Oracle dplyr works ──────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'odbc'
  Backtrace:
      ▆
   1. ├─testthat::skip_if_not("OracleODBC-19" %in% odbc::odbcListDataSources()$name) at test-zzz-dplyr.R:2:2
   2. │ └─base::isTRUE(condition)
   3. ├─"OracleODBC-19" %in% odbc::odbcListDataSources()$name
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-zzz-dplyr.R:186:3'): quantile translation works on Spark ───────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'odbc'
  Backtrace:
      ▆
   1. ├─testthat::skip_if_not("Databricks" %in% odbc::odbcListDataSources()$name) at test-zzz-dplyr.R:186:2
   2. │ └─base::isTRUE(condition)
   3. ├─"Databricks" %in% odbc::odbcListDataSources()$name
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-zzz-dplyr.R:244:3'): Oracle inSchema works ─────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'odbc'
  Backtrace:
      ▆
   1. ├─testthat::skip_if_not("OracleODBC-19" %in% odbc::odbcListDrivers()) at test-zzz-dplyr.R:244:2
   2. │ └─base::isTRUE(condition)
   3. ├─"OracleODBC-19" %in% odbc::odbcListDrivers()
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 14 | WARN 0 | SKIP 50 | PASS 286 ]
  Error: Test failures
  Execution halted