Last updated on 2026-05-13 16:50:40 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.1 | 7.41 | 873.34 | 880.75 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.1 | 5.16 | 73.07 | 78.23 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2.1 | 13.00 | 1350.08 | 1363.08 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.2.1 | 13.00 | 1476.63 | 1489.63 | OK | |
| r-devel-windows-x86_64 | 1.2.1 | 9.00 | 615.00 | 624.00 | OK | |
| r-patched-linux-x86_64 | 1.2.1 | 7.75 | 823.50 | 831.25 | OK | |
| r-release-linux-x86_64 | 1.2.1 | 7.23 | 828.01 | 835.24 | OK | |
| r-release-macos-arm64 | 1.2.1 | 2.00 | 149.00 | 151.00 | OK | |
| r-release-macos-x86_64 | 1.2.1 | 5.00 | 838.00 | 843.00 | OK | |
| r-release-windows-x86_64 | 1.2.1 | 9.00 | 606.00 | 615.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.1 | OK | ||||
| r-oldrel-macos-x86_64 | 1.2.1 | 5.00 | 400.00 | 405.00 | OK | |
| r-oldrel-windows-x86_64 | 1.2.1 | 12.00 | 915.00 | 927.00 | OK |
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [19s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(IncidencePrevalence)
>
> test_check("IncidencePrevalence")
Starting 2 test processes.
Saving _problems/test-estimatePrevalence-3.R
Saving _problems/test-estimatePrevalence-1221.R
Saving _problems/test-estimatePrevalence-1269.R
Saving _problems/test-generateDenominatorCohortSet-2.R
Saving _problems/test-generateDenominatorCohortSet-71.R
Saving _problems/test-generateDenominatorCohortSet-2455.R
Saving _problems/test-estimateIncidence-2.R
Saving _problems/test-estimateIncidence-1022.R
[ FAIL 8 | WARN 0 | SKIP 101 | PASS 0 ]
══ Skipped tests (101) ═════════════════════════════════════════════════════════
• On CRAN (101): 'test-dateUtilities.R:2:3',
'test-benchmarkIncidencePrevalence.R:2:3',
'test-benchmarkIncidencePrevalence.R:45:3', 'test-estimatePrevalence.R:41:3',
'test-estimatePrevalence.R:93:3', 'test-estimatePrevalence.R:150:3',
'test-estimatePrevalence.R:269:3', 'test-estimatePrevalence.R:413:3',
'test-estimatePrevalence.R:495:3', 'test-estimatePrevalence.R:646:3',
'test-estimatePrevalence.R:697:3', 'test-estimatePrevalence.R:742:3',
'test-estimatePrevalence.R:797:3', 'test-estimatePrevalence.R:845:3',
'test-estimatePrevalence.R:869:3', 'test-estimatePrevalence.R:894:3',
'test-estimatePrevalence.R:1035:3', 'test-estimatePrevalence.R:1082:3',
'test-estimatePrevalence.R:1115:3', 'test-estimatePrevalence.R:1194:3',
'test-estimatePrevalence.R:1246:3', 'test-estimatePrevalence.R:1416:3',
'test-estimatePrevalence.R:1458:3', 'test-estimatePrevalence.R:1504:3',
'test-estimatePrevalence.R:1556:3', 'test-estimatePrevalence.R:1672:3',
'test-generateDenominatorCohortSet.R:138:3',
'test-generateDenominatorCohortSet.R:185:3',
'test-generateDenominatorCohortSet.R:289:3',
'test-generateDenominatorCohortSet.R:326:3',
'test-generateDenominatorCohortSet.R:591:3',
'test-generateDenominatorCohortSet.R:641:3',
'test-generateDenominatorCohortSet.R:720:3',
'test-generateDenominatorCohortSet.R:812:3',
'test-generateDenominatorCohortSet.R:855:3',
'test-generateDenominatorCohortSet.R:907:3',
'test-generateDenominatorCohortSet.R:991:3',
'test-generateDenominatorCohortSet.R:1118:3',
'test-generateDenominatorCohortSet.R:1199:3',
'test-generateDenominatorCohortSet.R:1263:3',
'test-generateDenominatorCohortSet.R:1316:3',
'test-generateDenominatorCohortSet.R:1374:3',
'test-generateDenominatorCohortSet.R:1449:3',
'test-generateDenominatorCohortSet.R:1572:3',
'test-generateDenominatorCohortSet.R:1673:3',
'test-generateDenominatorCohortSet.R:1726:3',
'test-generateDenominatorCohortSet.R:1789:3',
'test-generateDenominatorCohortSet.R:2018:3',
'test-generateDenominatorCohortSet.R:2109:3',
'test-generateDenominatorCohortSet.R:2309:3',
'test-generateDenominatorCohortSet.R:2413:3',
'test-estimateIncidence.R:57:3', 'test-estimateIncidence.R:120:3',
'test-estimateIncidence.R:230:3', 'test-estimateIncidence.R:300:3',
'test-estimateIncidence.R:399:3', 'test-estimateIncidence.R:503:3',
'test-estimateIncidence.R:598:3', 'test-estimateIncidence.R:762:3',
'test-estimateIncidence.R:869:3', 'test-estimateIncidence.R:1063:3',
'test-estimateIncidence.R:1127:3', 'test-estimateIncidence.R:1184:3',
'test-estimateIncidence.R:1269:3', 'test-estimateIncidence.R:1413:3',
'test-estimateIncidence.R:1529:3', 'test-estimateIncidence.R:1608:3',
'test-estimateIncidence.R:1716:3', 'test-estimateIncidence.R:1820:3',
'test-estimateIncidence.R:1979:3', 'test-estimateIncidence.R:2035:3',
'test-estimateIncidence.R:2233:3', 'test-estimateIncidence.R:2432:3',
'test-estimateIncidence.R:2517:3', 'test-estimateIncidence.R:2943:3',
'test-estimateIncidence.R:2991:3', 'test-estimateIncidence.R:3046:3',
'test-estimateIncidence.R:3104:3', 'test-estimateIncidence.R:3127:3',
'test-estimateIncidence.R:3142:3', 'test-estimateIncidence.R:3182:3',
'test-estimateIncidence.R:3344:3', 'test-estimateIncidence.R:3423:3',
'test-estimateIncidence.R:3467:3', 'test-estimateIncidence.R:3513:3',
'test-estimateIncidence.R:3561:3', 'test-getStudyDays.R:2:3',
'test-getStudyDays.R:238:3', 'test-mockIncidencePrevalence.R:2:3',
'test-mockIncidencePrevalence.R:39:3', 'test-mockIncidencePrevalence.R:69:3',
'test-mockIncidencePrevalence.R:171:3', 'test-plotting.R:2:3',
'test-plotting.R:203:3', 'test-plotting.R:252:3', 'test-plotting.R:302:3',
'test-plotting.R:366:3', 'test-tables.R:2:3', 'test-tables.R:126:3',
'test-tidyResults.R:2:3', 'test-tidyResults.R:57:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-estimatePrevalence.R:2:3'): mock db: check output format ───────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence()`: The package "duckdb" is required.
Backtrace:
▆
1. ├─mockIncidencePrevalence() %>% ... at test-estimatePrevalence.R:2:3
2. ├─IncidencePrevalence::generateDenominatorCohortSet(., name = "denominator")
3. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...)
4. │ └─IncidencePrevalence:::checkInputGenerateDCS(...)
5. │ └─omopgenerics::validateCdmArgument(cdm)
6. │ └─omopgenerics::assertClass(...)
7. │ ├─omopgenerics:::checkClass(...)
8. │ ├─omopgenerics:::checkLength(...)
9. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
10. │ └─omopgenerics:::createCheckObject(x)
11. └─IncidencePrevalence::mockIncidencePrevalence()
12. └─rlang::check_installed("duckdb")
── Error ('test-estimatePrevalence.R:1221:3'): mock db: if missing cohort attributes ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence()`: The package "duckdb" is required.
Backtrace:
▆
1. └─IncidencePrevalence::mockIncidencePrevalence() at test-estimatePrevalence.R:1221:3
2. └─rlang::check_installed("duckdb")
── Error ('test-estimatePrevalence.R:1266:3'): mock db: prevalence using strata vars ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence(sampleSize = 1000, outPre = 0.7)`: The package "duckdb" is required.
Backtrace:
▆
1. └─IncidencePrevalence::mockIncidencePrevalence(...) at test-estimatePrevalence.R:1266:3
2. └─rlang::check_installed("duckdb")
── Error ('test-generateDenominatorCohortSet.R:2:3'): mock db: check output format ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence()`: The package "duckdb" is required.
Backtrace:
▆
1. └─IncidencePrevalence::mockIncidencePrevalence() at test-generateDenominatorCohortSet.R:2:3
2. └─rlang::check_installed("duckdb")
── Error ('test-generateDenominatorCohortSet.R:68:3'): mock db: checks on working example ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence(personTable = personTable, observationPeriodTable = observationPeriodTable)`: The package "duckdb" is required.
Backtrace:
▆
1. └─IncidencePrevalence::mockIncidencePrevalence(...) at test-generateDenominatorCohortSet.R:68:3
2. └─rlang::check_installed("duckdb")
── Error ('test-generateDenominatorCohortSet.R:2455:3'): mock db: target cohort extra columns ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence()`: The package "duckdb" is required.
Backtrace:
▆
1. └─IncidencePrevalence::mockIncidencePrevalence() at test-generateDenominatorCohortSet.R:2455:3
2. └─rlang::check_installed("duckdb")
── Error ('test-estimateIncidence.R:2:3'): mock db: check output format ────────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence()`: The package "duckdb" is required.
Backtrace:
▆
1. └─IncidencePrevalence::mockIncidencePrevalence() at test-estimateIncidence.R:2:3
2. └─rlang::check_installed("duckdb")
── Error ('test-estimateIncidence.R:1020:3'): mock db: multiple denominator inputs ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence(sampleSize = 6000, maxOutcomeDays = 5, maxOutcomes = 6)`: The package "duckdb" is required.
Backtrace:
▆
1. └─IncidencePrevalence::mockIncidencePrevalence(...) at test-estimateIncidence.R:1020:3
2. └─rlang::check_installed("duckdb")
[ FAIL 8 | WARN 0 | SKIP 101 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’ using rmarkdown
Quitting from a01_Introduction_to_IncidencePrevalence.Rmd:42-47 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `mockIncidencePrevalence()`:
! The package "duckdb" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a01_Introduction_to_IncidencePrevalence.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’
--- re-building ‘a02_Creating_denominator_populations.Rmd’ using rmarkdown
Quitting from a02_Creating_denominator_populations.Rmd:82-84 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `mockIncidencePrevalence()`:
! The package "duckdb" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a02_Creating_denominator_populations.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building ‘a02_Creating_denominator_populations.Rmd’
--- re-building ‘a03_Creating_target_denominator_populations.Rmd’ using rmarkdown
Quitting from a03_Creating_target_denominator_populations.Rmd:33-85 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `mockIncidencePrevalence()`:
! The package "duckdb" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a03_Creating_target_denominator_populations.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building ‘a03_Creating_target_denominator_populations.Rmd’
--- re-building ‘a04_Calculating_prevalence.Rmd’ using rmarkdown
Quitting from a04_Calculating_prevalence.Rmd:47-71 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `mockIncidencePrevalence()`:
! The package "duckdb" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a04_Calculating_prevalence.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building ‘a04_Calculating_prevalence.Rmd’
--- re-building ‘a05_Calculating_incidence.Rmd’ using rmarkdown
Quitting from a05_Calculating_incidence.Rmd:76-100 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `mockIncidencePrevalence()`:
! The package "duckdb" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a05_Calculating_incidence.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building ‘a05_Calculating_incidence.Rmd’
--- re-building ‘a06_Working_with_IncidencePrevalence_Results.Rmd’ using rmarkdown
Quitting from a06_Working_with_IncidencePrevalence_Results.Rmd:30-70 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `mockIncidencePrevalence()`:
! The package "duckdb" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a06_Working_with_IncidencePrevalence_Results.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building ‘a06_Working_with_IncidencePrevalence_Results.Rmd’
--- re-building ‘a07_benchmark.Rmd’ using rmarkdown
--- finished re-building ‘a07_benchmark.Rmd’
SUMMARY: processing the following files failed:
‘a01_Introduction_to_IncidencePrevalence.Rmd’
‘a02_Creating_denominator_populations.Rmd’
‘a03_Creating_target_denominator_populations.Rmd’
‘a04_Calculating_prevalence.Rmd’ ‘a05_Calculating_incidence.Rmd’
‘a06_Working_with_IncidencePrevalence_Results.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc