• using R Under development (unstable) (2026-09-10 r90517)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 23.1.1     flang version 23.1.1
• running under: Fedora Linux 44 (Server Edition)
• using session charset: UTF-8 * current time: 2026-09-10 15:26:42 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘CohortSurvival/DESCRIPTION’ ... OK
• this is package ‘CohortSurvival’ version ‘1.1.2’
• 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 ‘CohortSurvival’ can be installed ... OK See the install log for details.
• 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 ... 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... ERROR   Running ‘testthat.R’ 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")   Saving _problems/test-estimateSurvival-2615.R   Saving _problems/test-plotSurvival-176.R   Saving _problems/test-reexports-omopgenerics-43.R   [ FAIL 3 | WARN 0 | SKIP 69 | PASS 9 ]      ══ Skipped tests (69) ══════════════════════════════════════════════════════════   • On CRAN (69): '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-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-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:1314:3',     'test-estimateSurvival.R:1426:3', 'test-estimateSurvival.R:1448:3',     'test-estimateSurvival.R:1515:3', 'test-estimateSurvival.R:1700:3',     'test-estimateSurvival.R:1813:3', 'test-estimateSurvival.R:1843:3',     'test-estimateSurvival.R:1862:3', 'test-estimateSurvival.R:1895:3',     'test-estimateSurvival.R:2024:3', 'test-estimateSurvival.R:2244:3',     'test-estimateSurvival.R:2321:3', 'test-estimateSurvival.R:2377:5',     'test-estimateSurvival.R:2397:3', 'test-estimateSurvival.R:2442:3',     'test-estimateSurvival.R:2464:3', 'test-estimateSurvival.R:2488:3',     'test-estimateSurvival.R:2544:3', 'test-estimateSurvival.R:2596:3',     'test-estimateSurvival.R:2636:3', 'test-estimateSurvival.R:2668:3',     '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:94:3', 'test-tableSurvival.R:124:3',     'test-tableSurvival.R:148:3', 'test-tableSurvival.R:158:3',     'test-tableSurvivalAttrition.R:2:3',     'test-validateExtractSurvivalInputs.R:2:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-estimateSurvival.R:2615:3'): cohort id or cohort name as inputs ──   <rlib_error_package_not_found/rlang_error/error/condition>   Error in `mockMGUS2cdm()`: The package "duckdb" is required.   Backtrace:       ▆    1. └─CohortSurvival::mockMGUS2cdm() at test-estimateSurvival.R:2615:3    2. └─rlang::check_installed("duckdb")   ── Error ('test-plotSurvival.R:176:3'): plot with bound results with different hidden inputs ──   <rlib_error_package_not_found/rlang_error/error/condition>   Error in `mockMGUS2cdm()`: The package "duckdb" is required.   Backtrace:       ▆    1. └─CohortSurvival::mockMGUS2cdm() at test-plotSurvival.R:176:3    2. └─rlang::check_installed("duckdb")   ── Error ('test-reexports-omopgenerics.R:43:3'): omopgenerics filterSettings ───   <rlib_error_package_not_found/rlang_error/error/condition>   Error in `mockMGUS2cdm()`: The package "duckdb" is required.   Backtrace:       ▆    1. └─CohortSurvival::mockMGUS2cdm() at test-reexports-omopgenerics.R:43:3    2. └─rlang::check_installed("duckdb")      [ FAIL 3 | WARN 0 | SKIP 69 | PASS 9 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘a00_Creating_cohorts_for_survival.Rmd’ using rmarkdown Quitting from a00_Creating_cohorts_for_survival.Rmd:30-32 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlib_error_package_not_found> Error in `CohortSurvival::mockMGUS2cdm()`: ! The package "duckdb" is required. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'a00_Creating_cohorts_for_survival.Rmd' failed with diagnostics: The package "duckdb" is required. --- failed re-building ‘a00_Creating_cohorts_for_survival.Rmd’ --- re-building ‘a01_Single_event_of_interest.Rmd’ using rmarkdown Quitting from a01_Single_event_of_interest.Rmd:31-33 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlib_error_package_not_found> Error in `CohortSurvival::mockMGUS2cdm()`: ! The package "duckdb" is required. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'a01_Single_event_of_interest.Rmd' failed with diagnostics: The package "duckdb" is required. --- 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/rlib_error_package_not_found> Error in `CohortSurvival::mockMGUS2cdm()`: ! The package "duckdb" is required. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'a02_Competing_risk_survival.Rmd' failed with diagnostics: The package "duckdb" is required. --- 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/rlib_error_package_not_found> Error in `CohortSurvival::mockMGUS2cdm()`: ! The package "duckdb" is required. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'a03_Further_survival_analyses.Rmd' failed with diagnostics: The package "duckdb" is required. --- failed re-building ‘a03_Further_survival_analyses.Rmd’ SUMMARY: processing the following files failed:   ‘a00_Creating_cohorts_for_survival.Rmd’   ‘a01_Single_event_of_interest.Rmd’ ‘a02_Competing_risk_survival.Rmd’   ‘a03_Further_survival_analyses.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