Last updated on 2026-05-13 01:49:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 7.11 | 998.58 | 1005.69 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 4.50 | 66.58 | 71.08 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 11.00 | 1554.82 | 1565.82 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 11.00 | 1566.11 | 1577.11 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 9.00 | 670.00 | 679.00 | OK | |
| r-patched-linux-x86_64 | 1.1.0 | 6.48 | 944.59 | 951.07 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 5.45 | 956.43 | 961.88 | OK | |
| r-release-macos-arm64 | 1.1.0 | 2.00 | 166.00 | 168.00 | OK | |
| r-release-macos-x86_64 | 1.1.0 | 5.00 | 795.00 | 800.00 | OK | |
| r-release-windows-x86_64 | 1.1.0 | 8.00 | 661.00 | 669.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 2.00 | 155.00 | 157.00 | OK | |
| r-oldrel-macos-x86_64 | 1.1.0 | 4.00 | 621.00 | 625.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.0 | 11.00 | 1001.00 | 1012.00 | OK |
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [17s/14s]
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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.0
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-devel-linux-x86_64-debian-gcc