• using R version 4.6.1 (2026-06-24)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.2.0-3) 16.2.0     GNU Fortran (Debian 16.2.0-3) 16.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-10-10 03:55:25 UTC
• checking for file ‘CohortGenerator/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘CohortGenerator’ version ‘1.1.1’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• 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/3s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
• checking loading without being on the library search path ... [2s/3s] 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 ... [17s/24s] 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/3s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [5s/7s] ERROR   Running ‘testthat.R’ [5s/6s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(CohortGenerator)   Loading required package: DatabaseConnector   Loading required package: R6   >   > test_check("CohortGenerator")   attempting to download GiBleed   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      attempting to extract and load: /home/hornik/tmp/scratch/RtmpewroEY/GiBleed_5.3.zip to: /home/hornik/tmp/scratch/RtmpewroEY/GiBleed_5.3.sqlite   Error in `source_dir()`:   ! Failed to evaluate './setup.R'.   Caused by error:   ! not an error   Backtrace:        ▆     1. ├─testthat::test_check("CohortGenerator")     2. │ └─testthat::test_dir(...)     3. │ └─testthat:::test_files(...)     4. │ └─testthat:::test_files_serial(...)     5. │ └─testthat:::test_files_setup_state(...)     6. │ └─testthat::source_test_setup(".", env)     7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)     8. │ └─base::lapply(...)     9. │ └─testthat (local) FUN(X[[i]], ...)    10. │ └─testthat::source_file(...)    11. │ ├─base::withCallingHandlers(...)    12. │ └─base::eval(exprs, env)    13. │ └─base::eval(exprs, env)    14. │ └─Eunomia::getEunomiaConnectionDetails() at ./setup.R:2:1    15. │ └─Eunomia::getDatabaseFile(...)    16. │ └─Eunomia::extractLoadData(...)    17. │ └─Eunomia::loadDataFiles(...)    18. │ ├─DBI::dbExecute(conn = connection, statement = statement)    19. │ └─DBI::dbExecute(conn = connection, statement = statement)    20. │ ├─DBI::dbSendStatement(conn, statement, ...)    21. │ └─DBI::dbSendStatement(conn, statement, ...)    22. │ ├─DBI::dbSendQuery(conn, statement, ...)    23. │ └─RSQLite::dbSendQuery(conn, statement, ...)    24. │ └─RSQLite (local) .local(conn, statement, ...)    25. │ ├─methods::new(...)    26. │ │ ├─methods::initialize(value, ...)    27. │ │ └─methods::initialize(value, ...)    28. │ └─RSQLite:::result_create(conn@ptr, statement)    29. └─base::.handleSimpleError(`<fn>`, "not an error", base::quote(NULL))    30. └─testthat (local) h(simpleError(msg, call))    31. └─cli::cli_abort(...)    32. └─rlang::abort(...)   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [30s/43s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘CreatingCohortSubsetDefinitions.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished 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 Quitting from GeneratingCohorts.Rmd:122-144 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! not an error --- Backtrace:      x   1. \-Eunomia::getEunomiaConnectionDetails()   2. \-Eunomia::getDatabaseFile(...)   3. \-Eunomia::extractLoadData(...)   4. \-Eunomia::loadDataFiles(...)   5. +-DBI::dbExecute(conn = connection, statement = statement)   6. \-DBI::dbExecute(conn = connection, statement = statement)   7. +-DBI::dbSendStatement(conn, statement, ...)   8. \-DBI::dbSendStatement(conn, statement, ...)   9. +-DBI::dbSendQuery(conn, statement, ...)  10. \-RSQLite::dbSendQuery(conn, statement, ...)  11. \-RSQLite (local) .local(conn, statement, ...)  12. +-methods::new(...)  13. | +-methods::initialize(value, ...)  14. | \-methods::initialize(value, ...)  15. \-RSQLite:::result_create(conn@ptr, statement) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'GeneratingCohorts.Rmd' failed with diagnostics: not an error --- failed 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 Quitting from UsingTemplateCohorts.Rmd:40-72 [unnamed-chunk-1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! not an error --- Backtrace:      ▆   1. ├─DatabaseConnector::connect(Eunomia::getEunomiaConnectionDetails())   2. └─Eunomia::getEunomiaConnectionDetails()   3. └─Eunomia::getDatabaseFile(...)   4. └─Eunomia::extractLoadData(...)   5. └─Eunomia::loadDataFiles(...)   6. ├─DBI::dbExecute(conn = connection, statement = statement)   7. └─DBI::dbExecute(conn = connection, statement = statement)   8. ├─DBI::dbSendStatement(conn, statement, ...)   9. └─DBI::dbSendStatement(conn, statement, ...)  10. ├─DBI::dbSendQuery(conn, statement, ...)  11. └─RSQLite::dbSendQuery(conn, statement, ...)  12. └─RSQLite (local) .local(conn, statement, ...)  13. ├─methods::new(...)  14. │ ├─methods::initialize(value, ...)  15. │ └─methods::initialize(value, ...)  16. └─RSQLite:::result_create(conn@ptr, statement) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'UsingTemplateCohorts.Rmd' failed with diagnostics: not an error --- failed re-building ‘UsingTemplateCohorts.Rmd’ SUMMARY: processing the following files failed:   ‘GeneratingCohorts.Rmd’ ‘UsingTemplateCohorts.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [9s/13s] OK
• checking HTML version of manual ... [6s/10s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs