* using log directory ‘/data/localhost/ripley/R/packages/tests-donttest/TreatmentPatterns.Rcheck’ * using R Under development (unstable) (2026-08-22 r90441) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-08-23 05:03:10 UTC * checking for file ‘TreatmentPatterns/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TreatmentPatterns’ version ‘3.1.2’ * 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 ‘TreatmentPatterns’ can be installed ... 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 ... [8s/11s] 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 examples with --run-donttest ... [96s/247s] ERROR Running examples in ‘TreatmentPatterns-Ex.R’ failed The error most likely occurred in: > ### Name: export > ### Title: export > ### Aliases: export > > ### ** Examples > > ## No test: > ableToRun <- all( + require("CirceR", character.only = TRUE, quietly = TRUE), + require("CDMConnector", character.only = TRUE, quietly = TRUE), + require("TreatmentPatterns", character.only = TRUE, quietly = TRUE), + require("dplyr", character.only = TRUE, quietly = TRUE) + ) Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union > > if (ableToRun) { + library(TreatmentPatterns) + library(CDMConnector) + library(dplyr) + + withr::local_envvar( + R_USER_CACHE_DIR = tempfile(), + EUNOMIA_DATA_FOLDER = Sys.getenv("EUNOMIA_DATA_FOLDER", unset = tempfile()) + ) + + tryCatch({ + if (Sys.getenv("skip_eunomia_download_test") != "TRUE") { + CDMConnector::downloadEunomiaData(overwrite = TRUE) + } + }, error = function(e) NA) + + con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomiaDir()) + cdm <- cdmFromCon(con, cdmSchema = "main", writeSchema = "main") + + cohortSet <- readCohortSet( + path = system.file(package = "TreatmentPatterns", "exampleCohorts") + ) + + cdm <- generateCohortSet( + cdm = cdm, + cohortSet = cohortSet, + name = "cohort_table" + ) + + cohorts <- cohortSet %>% + # Remove 'cohort' and 'json' columns + select(-"cohort", -"json") %>% + mutate(type = c("event", "event", "event", "event", "exit", "event", "event", "target")) %>% + rename( + cohortId = "cohort_definition_id", + cohortName = "cohort_name", + ) %>% + select("cohortId", "cohortName", "type") + + outputEnv <- computePathways( + cohorts = cohorts, + cohortTableName = "cohort_table", + cdm = cdm + ) + + results <- export( + andromeda = outputEnv + ) + + Andromeda::close(outputEnv) + DBI::dbDisconnect(con, shutdown = TRUE) + } trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/GiBleed_5.3.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Download completed! Error: ‘readr’ must be installed for this functionality. Execution halted Ran 3/3 deferred expressions * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [17s/26s] [17s/26s] ERROR 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(TreatmentPatterns) > > test_check("TreatmentPatterns") Starting 2 test processes. Error: ! testthat subprocess failed to start. trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/GiBleed_5.3.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) = = = == === === ==== ====== = === ===== = == == ==== = == ==== ==== downloaded 6.4 MB Download completed! duckdb is storing downloaded extensions and secrets under ~/.duckdb: ℹ /data/localhost/ripley/.duckdb This persists across sessions and is shared with the DuckDB CLI and other clients. ℹ Run duckdb(shared_home = FALSE) to use a temporary directory inst ead. ℹ See ?duckdb_storage for details and alternatives. Creating CDM database /tmp/Rtmp6aZzWu/working_dir/RtmpfUWNbB/eunomiaData/GiBleed_5.3.zip duckdb is storing downloaded extensions and secrets under ~/.duckdb: ℹ /data/localhost/ripley/.duckdb This persists across sessions and is shared with the DuckDB CLI and other clients. ℹ Run duckdb(shared_home = FALSE) to use a temporary directory instead. ℹ See ?duckdb_storage for details and alternatives. Error in `source_dir()`: ! Failed to evaluate './setup.R'. Caused by error: ! 'readr' must be installed for this functionality. Backtrace: ▆ 1. ├─global callr_startup_hook() 2. │ └─asNamespace("testthat")$queue_process_setup(...) 3. │ └─asNamespace("testthat")$test_files_setup_state(...) 4. │ └─testthat::source_test_setup(".", env) 5. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE) 6. │ └─base::lapply(...) 7. │ └─testthat (local) FUN(X[[i]], ...) 8. │ └─testthat::source_file(...) 9. │ ├─base::withCallingHandlers(...) 10. │ └─base::eval(exprs, env) 11. │ └─base::eval(exprs, env) 12. │ └─TreatmentPatterns:::generateCohortTableCDMC() at ./setup.R:36:3 13. │ └─CDMConnector::readCohortSet(...) at ./helper-generateCohortTableCDMC.R:17:5 14. │ └─CDMConnector:::ensureInstalled("readr") 15. │ └─base::stop(msg, call. = FALSE) 16. └─base::.handleSimpleError(...) 17. └─testthat (local) h(simpleError(msg, call)) 18. └─cli::cli_abort(...) 19. └─rlang::abort(...) Ran 4/4 deferred expressions No deferred expressions to run Backtrace: ▆ 1. └─testthat::test_check("TreatmentPatterns") 2. └─testthat::test_dir(...) 3. └─testthat:::test_files(...) 4. └─testthat:::test_files_parallel(...) 5. ├─withr::with_dir(...) 6. │ └─base::force(code) 7. ├─testthat::with_reporter(...) 8. │ └─base::tryCatch(...) 9. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 10. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 12. └─testthat:::parallel_event_loop_chunky(queue, reporters, ".") 13. └─queue$poll(Inf) 14. └─base::lapply(...) 15. └─testthat (local) FUN(X[[i]], ...) 16. └─private$handle_error(msg, i) 17. └─cli::cli_abort(...) 18. └─rlang::abort(...) Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [15s/29s] ERROR Error(s) in re-building vignettes: --- re-building ‘a000_bestPractices.Rmd’ using rmarkdown --- finished re-building ‘a000_bestPractices.Rmd’ --- re-building ‘a001_DefiningCohorts.Rmd’ using rmarkdown --- finished re-building ‘a001_DefiningCohorts.Rmd’ --- re-building ‘a010_Computing_Pathways.Rmd’ using rmarkdown Quitting from a010_Computing_Pathways.Rmd:46-64 [unnamed-chunk-1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! 'readr' must be installed for this functionality. --- Backtrace: ▆ 1. └─CDMConnector::readCohortSet(...) 2. └─CDMConnector:::ensureInstalled("readr") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'a010_Computing_Pathways.Rmd' failed with diagnostics: 'readr' must be installed for this functionality. --- failed re-building ‘a010_Computing_Pathways.Rmd’ --- re-building ‘a020_Exporting.Rmd’ using rmarkdown --- finished re-building ‘a020_Exporting.Rmd’ --- re-building ‘a030_Evaluating_Output.Rmd’ using rmarkdown Quitting from a030_Evaluating_Output.Rmd:31-88 [setup_treatment_patterns] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! 'readr' must be installed for this functionality. --- Backtrace: ▆ 1. └─CDMConnector::readCohortSet(...) 2. └─CDMConnector:::ensureInstalled("readr") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'a030_Evaluating_Output.Rmd' failed with diagnostics: 'readr' must be installed for this functionality. --- failed re-building ‘a030_Evaluating_Output.Rmd’ --- re-building ‘a998_Strategus.Rmd’ using rmarkdown --- finished re-building ‘a998_Strategus.Rmd’ --- re-building ‘a999_Publications-Presentations.Rmd’ using rmarkdown --- finished re-building ‘a999_Publications-Presentations.Rmd’ SUMMARY: processing the following files failed: ‘a010_Computing_Pathways.Rmd’ ‘a030_Evaluating_Output.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 * checking for new files in some other directories ... OK * DONE Status: 3 ERRORs See ‘/data/localhost/ripley/R/packages/tests-donttest/TreatmentPatterns.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 6:48.95, 167.36 + 25.38