Running ‘testthat.R’ [17s/15s]
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.
  Saving _problems/test-addCohortSurvival-814.R
  Saving _problems/test-plotSurvival-173.R
  Saving _problems/test-plotSurvival-196.R
  Saving _problems/test-reexports-omopgenerics-43.R
  Saving _problems/test-estimateSurvival-2.R
  Saving _problems/test-estimateSurvival-2167.R
  Saving _problems/test-estimateSurvival-2242.R
  Saving _problems/test-estimateSurvival-2286.R
  Saving _problems/test-estimateSurvival-2307.R
  Saving _problems/test-estimateSurvival-2330.R
  Saving _problems/test-estimateSurvival-2385.R
  Saving _problems/test-estimateSurvival-2396.R
  Saving _problems/test-estimateSurvival-2414.R
  [ FAIL 13 | WARN 0 | SKIP 56 | PASS 0 ]
  
  ══ Skipped tests (56) ══════════════════════════════════════════════════════════
  • On CRAN (56): 'test-asSurvivalResult.R:2:3', 'test-asSurvivalResult.R:19:3',
    'test-asSurvivalResult.R:54:3', 'test-asSurvivalResult.R:94:3',
    'test-asSurvivalResult.R:148:3', 'test-asSurvivalResult.R:203:3',
    'test-asSurvivalResult.R:246:3', 'test-asSurvivalResult.R:289:3',
    'test-asSurvivalResult.R:330:3', 'test-addCohortSurvival.R:2:3',
    'test-addCohortSurvival.R:73:3', 'test-addCohortSurvival.R:160:3',
    'test-addCohortSurvival.R:259:3', 'test-addCohortSurvival.R:351:3',
    'test-addCohortSurvival.R:455:3', 'test-addCohortSurvival.R:541:3',
    'test-addCohortSurvival.R:633:3', 'test-addCohortSurvival.R:712:3',
    'test-mockMGUS2cdm.R:2:3', 'test-plotSurvival.R:2:3',
    'test-plotSurvival.R:19:3', 'test-plotSurvival.R:52:3',
    'test-plotSurvival.R:83:3', 'test-plotSurvival.R:126:3',
    'test-plotSurvival.R:134:3', 'test-plotSurvival.R:157:3',
    'test-plotSurvival.R:186:3', '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-estimateSurvival.R:80:3',
    'test-estimateSurvival.R:131:3', 'test-estimateSurvival.R:193:3',
    'test-estimateSurvival.R:351:3', 'test-estimateSurvival.R:556:3',
    'test-estimateSurvival.R:698:3', 'test-estimateSurvival.R:1166:3',
    'test-estimateSurvival.R:1278:3', 'test-estimateSurvival.R:1300:3',
    'test-estimateSurvival.R:1367:3', 'test-estimateSurvival.R:1552:3',
    'test-estimateSurvival.R:1665:3', 'test-estimateSurvival.R:1695:3',
    'test-estimateSurvival.R:1714:3', 'test-estimateSurvival.R:1747:3',
    'test-estimateSurvival.R:1876:3', 'test-estimateSurvival.R:2090:3',
    'test-estimateSurvival.R:2222:5', 'test-estimateSurvival.R:2435:3',
    'test-estimateSurvival.R:2467:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-addCohortSurvival.R:814:3'): cohort id or cohort name ──────────
  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. ├─DBI::dbConnect(duckdb::duckdb(), ":memory:") at test-addCohortSurvival.R:814:3
   2. ├─base::loadNamespace(x)
   3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
   5. │ │   └─base (local) doWithOneRestart(return(expr), restart)
   6. │ └─base::stop(cond)
   7. └─base (local) `<fn>`(`<pckgNtFE>`)
  ── Error ('test-plotSurvival.R:173:3'): 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:173:3
   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-plotSurvival.R:196:3'): expected errors for available columns and plot ──
  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:196:3
   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:2:3'): mgus example: no Competing risk ──────
  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:2:3
   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:2167:5'): mgus example: empty outcome tables or cohorts ──
  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:2167:5
   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:2242:5'): no outcomes among cohort ──────────
  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:2242:5
   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:2286:3'): tables from cdm do not change after estimation ──
  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:2286:3
   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:2307:3'): median survival is NA when it cannot be estimated completely ──
  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:2307:3
   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:2330:3'): empty input cohort after input filtering ──
  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:2330:3
   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:2385:3'): empty input cohort before input filtering ──
  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:2385:3
   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:2396:3'): multiple strata names ─────────────
  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:2396:3
   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:2414:3'): 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:2414:3
   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 13 | WARN 0 | SKIP 56 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted