* using log directory ‘/data/localhost/ripley/R/packages/tests-clang-trunk/IncidencePrevalence.Rcheck’ * using R Under development (unstable) (2026-09-03 r90476) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 23.1.0 flang version 23.1.0 * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-09-03 07:59:07 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘IncidencePrevalence/DESCRIPTION’ ... OK * this is package ‘IncidencePrevalence’ version ‘1.2.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: ‘duckdb’ * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘IncidencePrevalence’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [10s/12s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [19s/18s] [19s/19s] ERROR 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-benchmarkIncidencePrevalence.R:2:3', 'test-benchmarkIncidencePrevalence.R:45:3', 'test-dateUtilities.R:2:3', '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 ─────── 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:::checkEmpty(...) 8. │ ├─omopgenerics:::checkClass(...) 9. │ ├─omopgenerics:::checkLength(...) 10. │ ├─omopgenerics:::checkNull(createCheckObject(x), null) 11. │ └─omopgenerics:::createCheckObject(x) 12. └─IncidencePrevalence::mockIncidencePrevalence() 13. └─rlang::check_installed("duckdb") ── Error ('test-estimatePrevalence.R:1221:3'): mock db: if missing cohort attributes ── 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 ── 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 ── 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 ── 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 ── 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 ──────── 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 ── 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [13s/15s] 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 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 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 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 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 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 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 * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs See ‘/data/localhost/ripley/R/packages/tests-clang-trunk/IncidencePrevalence.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:29.38, 68.68 + 7.65