Running ‘testthat.R’ [21s/19s]
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(CohortSurvival)
  > 
  > test_check("CohortSurvival")
  Starting 2 test processes.
  > test-competing-risk-guard.R: 
  > test-competing-risk-guard.R: -- No results for competing risk analysis --------------------------------------
  > test-competing-risk-guard.R: Competing risk variable must have three levels.Do you have at least 1
  > test-competing-risk-guard.R: individual for:
  > test-competing-risk-guard.R: * 1) censored without event,
  > test-competing-risk-guard.R: * 2) censored at outcome event of intest, and
  > test-competing-risk-guard.R: * 3) censored at outcome competing event?
  Saving _problems/test-plotSurvival-176.R
  Saving _problems/test-reexports-omopgenerics-43.R
  Saving _problems/test-estimateSurvival-2551.R
  [ FAIL 3 | WARN 0 | SKIP 69 | PASS 9 ]
  
  ══ Skipped tests (69) ══════════════════════════════════════════════════════════
  • On CRAN (69): 'test-asSurvivalResult.R:2:3', 'test-asSurvivalResult.R:41:3',
    'test-asSurvivalResult.R:76:3', 'test-asSurvivalResult.R:116:3',
    'test-asSurvivalResult.R:170:3', 'test-asSurvivalResult.R:225:3',
    'test-asSurvivalResult.R:268:3', 'test-asSurvivalResult.R:311:3',
    'test-asSurvivalResult.R:352:3', 'test-addCohortSurvival.R:2:3',
    'test-addCohortSurvival.R:73:3', 'test-addCohortSurvival.R:159:3',
    'test-addCohortSurvival.R:246:3', 'test-addCohortSurvival.R:345:3',
    'test-addCohortSurvival.R:454:3', 'test-addCohortSurvival.R:558:3',
    'test-addCohortSurvival.R:644:3', 'test-addCohortSurvival.R:736:3',
    'test-addCohortSurvival.R:815:3', 'test-addCohortSurvival.R:917:3',
    'test-mockMGUS2cdm.R:2:3', 'test-plotSurvival.R:2:3',
    'test-plotSurvival.R:22:3', 'test-plotSurvival.R:55:3',
    'test-plotSurvival.R:86:3', 'test-plotSurvival.R:129:3',
    'test-plotSurvival.R:137:3', 'test-plotSurvival.R:160:3',
    'test-plotSurvival.R:189:3', 'test-plotSurvival.R:199:3',
    'test-reexports-omopgenerics.R:3:3', 'test-riskTable.R:2:3',
    'test-riskTable.R:65:3', 'test-tableSurvival.R:2:3',
    'test-tableSurvival.R:91:3', 'test-tableSurvival.R:117:3',
    'test-tableSurvival.R:141:3', 'test-tableSurvival.R:151:3',
    'test-tableSurvivalAttrition.R:2:3',
    'test-validateExtractSurvivalInputs.R:2:3', 'test-estimateSurvival.R:2:3',
    'test-estimateSurvival.R:81:3', 'test-estimateSurvival.R:199:3',
    'test-estimateSurvival.R:250:3', 'test-estimateSurvival.R:312:3',
    'test-estimateSurvival.R:470:3', 'test-estimateSurvival.R:675:3',
    'test-estimateSurvival.R:817:3', 'test-estimateSurvival.R:1296:3',
    'test-estimateSurvival.R:1408:3', 'test-estimateSurvival.R:1430:3',
    'test-estimateSurvival.R:1497:3', 'test-estimateSurvival.R:1682:3',
    'test-estimateSurvival.R:1795:3', 'test-estimateSurvival.R:1825:3',
    'test-estimateSurvival.R:1844:3', 'test-estimateSurvival.R:1877:3',
    'test-estimateSurvival.R:2006:3', 'test-estimateSurvival.R:2220:3',
    'test-estimateSurvival.R:2297:3', 'test-estimateSurvival.R:2353:5',
    'test-estimateSurvival.R:2373:3', 'test-estimateSurvival.R:2418:3',
    'test-estimateSurvival.R:2440:3', 'test-estimateSurvival.R:2464:3',
    'test-estimateSurvival.R:2520:3', 'test-estimateSurvival.R:2532:3',
    'test-estimateSurvival.R:2572:3', 'test-estimateSurvival.R:2604:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plotSurvival.R:176:3'): plot with bound results with different hidden inputs ──
  Error in `(function (cond)  .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
  Backtrace:
      ▆
   1. ├─CohortSurvival::mockMGUS2cdm() at test-plotSurvival.R:176:3
   2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:")
   3. ├─base::loadNamespace(x)
   4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   6. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   7. │ └─base::stop(cond)
   8. └─base (local) `<fn>`(`<pckgNtFE>`)
  ── Error ('test-reexports-omopgenerics.R:43:3'): omopgenerics filterSettings ───
  Error in `(function (cond)  .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
  Backtrace:
      ▆
   1. ├─CohortSurvival::mockMGUS2cdm() at test-reexports-omopgenerics.R:43:3
   2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:")
   3. ├─base::loadNamespace(x)
   4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   6. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   7. │ └─base::stop(cond)
   8. └─base (local) `<fn>`(`<pckgNtFE>`)
  ── Error ('test-estimateSurvival.R:2551:3'): cohort id or cohort name as inputs ──
  Error in `(function (cond)  .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
  Backtrace:
      ▆
   1. ├─CohortSurvival::mockMGUS2cdm() at test-estimateSurvival.R:2551:3
   2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:")
   3. ├─base::loadNamespace(x)
   4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   6. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   7. │ └─base::stop(cond)
   8. └─base (local) `<fn>`(`<pckgNtFE>`)
  
  [ FAIL 3 | WARN 0 | SKIP 69 | PASS 9 ]
  Error:
  ! Test failures.
  Execution halted