• using R Under development (unstable) (2026-05-12 r90049)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16-20260425-1) 16.0.1 20260425 (prerelease) [gcc-16 r16-8812-gd9c07462a22]     GNU Fortran (Debian 16-20260425-1) 16.0.1 20260425 (prerelease) [gcc-16 r16-8812-gd9c07462a22]
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-05-13 12:29:10 UTC
• checking for file ‘CohortGenerator/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘CohortGenerator’ version ‘1.1.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/3s] OK
• 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 ‘CohortGenerator’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [2s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [1s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [2s/2s] 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 ... [11s/15s] OK
• checking Rd files ... [1s/1s] 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 ... [0s/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [2s/2s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [78s/102s] OK   Running ‘testthat.R’ [78s/101s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [40s/48s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘CreatingCohortSubsetDefinitions.Rmd’ using rmarkdown Quitting from CreatingCohortSubsetDefinitions.Rmd:190-212 [unnamed-chunk-8] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! 'duckdb' must be installed for this functionality. --- Backtrace:     ▆  1. └─DatabaseConnector::connect(duckdbConnectionDetails)  2. └─DatabaseConnector:::connectDuckdb(connectionDetails)  3. └─DatabaseConnector:::ensure_installed("duckdb") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'CreatingCohortSubsetDefinitions.Rmd' failed with diagnostics: 'duckdb' must be installed for this functionality. --- failed re-building ‘CreatingCohortSubsetDefinitions.Rmd’ --- re-building ‘GeneratingCohorts.Rmd’ using rmarkdown trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' Content type 'application/zip' length 6861852 bytes (6.5 MB) ================================================== downloaded 6.5 MB --- finished re-building ‘GeneratingCohorts.Rmd’ --- re-building ‘SamplingCohorts.Rmd’ using rmarkdown --- finished re-building ‘SamplingCohorts.Rmd’ --- re-building ‘UsingTemplateCohorts.Rmd’ using rmarkdown trying URL 'https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip' Content type 'application/zip' length 6861852 bytes (6.5 MB) ================================================== downloaded 6.5 MB --- finished re-building ‘UsingTemplateCohorts.Rmd’ SUMMARY: processing the following file failed:   ‘CreatingCohortSubsetDefinitions.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [4s/6s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR