Last updated on 2026-05-17 16:50:12 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.1 | 7.32 | 515.98 | 523.30 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.1 | 4.10 | 339.81 | 343.91 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.1 | 11.00 | 846.88 | 857.88 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.1 | 12.00 | 867.27 | 879.27 | OK | |
| r-devel-windows-x86_64 | 1.1.1 | 9.00 | 350.00 | 359.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 7.26 | 960.57 | 967.83 | OK | |
| r-release-linux-x86_64 | 1.1.1 | 6.60 | 85.26 | 91.86 | ERROR | |
| r-release-macos-arm64 | 1.1.1 | 2.00 | 86.00 | 88.00 | OK | |
| r-release-macos-x86_64 | 1.1.1 | 5.00 | 389.00 | 394.00 | OK | |
| r-release-windows-x86_64 | 1.1.1 | 9.00 | 363.00 | 372.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.1 | 2.00 | 96.00 | 98.00 | OK | |
| r-oldrel-macos-x86_64 | 1.1.1 | 4.00 | 331.00 | 335.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.1 | 11.00 | 476.00 | 487.00 | OK |
Version: 1.1.1
Check: tests
Result: ERROR
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
Flavor: r-release-linux-x86_64
Version: 1.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Single_event_of_interest.Rmd’ using rmarkdown
Quitting from a01_Single_event_of_interest.Rmd:31-33 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
---
Backtrace:
▆
1. ├─CohortSurvival::mockMGUS2cdm()
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: processing vignette 'a01_Single_event_of_interest.Rmd' failed with diagnostics:
error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
--- failed re-building ‘a01_Single_event_of_interest.Rmd’
--- re-building ‘a02_Competing_risk_survival.Rmd’ using rmarkdown
Quitting from a02_Competing_risk_survival.Rmd:31-33 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
---
Backtrace:
▆
1. ├─CohortSurvival::mockMGUS2cdm()
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: processing vignette 'a02_Competing_risk_survival.Rmd' failed with diagnostics:
error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
--- failed re-building ‘a02_Competing_risk_survival.Rmd’
--- re-building ‘a03_Further_survival_analyses.Rmd’ using rmarkdown
Quitting from a03_Further_survival_analyses.Rmd:31-33 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
---
Backtrace:
▆
1. ├─CohortSurvival::mockMGUS2cdm()
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: processing vignette 'a03_Further_survival_analyses.Rmd' failed with diagnostics:
error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
--- failed re-building ‘a03_Further_survival_analyses.Rmd’
SUMMARY: processing the following files failed:
‘a01_Single_event_of_interest.Rmd’ ‘a02_Competing_risk_survival.Rmd’
‘a03_Further_survival_analyses.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64