* using log directory ‘/data/localhost/ripley/R/packages/tests-clang-trunk/CohortSymmetry.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 07:59:05 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘CohortSymmetry/DESCRIPTION’ ... OK * this is package ‘CohortSymmetry’ version ‘0.3.0’ * 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 ‘CohortSymmetry’ 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 ... 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 ... Running ‘testthat.R’ 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/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(CohortSymmetry) > > test_check("CohortSymmetry") Saving _problems/test-generateSequenceCohortSet-37.R Saving _problems/test-generateSequenceCohortSet-80.R Saving _problems/test-plotTemporalSymmetry-18.R Saving _problems/test-summariseSequenceRatios-34.R Saving _problems/test-summariseSequenceRatios-100.R Saving _problems/test-summariseSequenceRatios-167.R Saving _problems/test-summariseTemporalSymmetry-3.R Saving _problems/test-tableSequenceRatios-4.R Saving _problems/test-tableTemporalSymmetry-4.R [ FAIL 9 | WARN 0 | SKIP 55 | PASS 0 ] ══ Skipped tests (55) ══════════════════════════════════════════════════════════ • On CRAN (55): 'test-attrition.R:2:3', 'test-attrition.R:63:3', 'test-attrition.R:149:3', 'test-attrition.R:310:3', 'test-attrition.R:397:3', 'test-attrition.R:461:3', 'test-attrition.R:592:3', 'test-attrition.R:769:3', 'test-dbs.R:2:3', 'test-dbs.R:50:3', 'test-eunomia.R:2:3', 'test-eunomia.R:65:3', 'test-generateSequenceCohortSet.R:3:3', 'test-generateSequenceCohortSet.R:20:3', 'test-generateSequenceCohortSet.R:59:3', 'test-generateSequenceCohortSet.R:99:3', 'test-generateSequenceCohortSet.R:156:3', 'test-generateSequenceCohortSet.R:208:3', 'test-generateSequenceCohortSet.R:262:3', 'test-generateSequenceCohortSet.R:291:3', 'test-generateSequenceCohortSet.R:333:3', 'test-generateSequenceCohortSet.R:359:3', 'test-generateSequenceCohortSet.R:430:3', 'test-generateSequenceCohortSet.R:518:3', 'test-generateSequenceCohortSet.R:666:3', 'test-generateSequenceCohortSet.R:754:3', 'test-generateSequenceCohortSet.R:767:3', 'test-generateSequenceCohortSet.R:779:3', 'test-generateSequenceCohortSet.R:791:3', 'test-generateSequenceCohortSet.R:803:3', 'test-generateSequenceCohortSet.R:821:3', 'test-generateSequenceCohortSet.R:839:3', 'test-generateSequenceCohortSet.R:851:3', 'test-generateSequenceCohortSet.R:862:3', 'test-generateSequenceCohortSet.R:873:3', 'test-generateSequenceCohortSet.R:897:3', 'test-plotSequenceRatio.R:2:3', 'test-plotSequenceRatio.R:42:3', 'test-plotSequenceRatio.R:80:3', 'test-plotTemporalSymmetry.R:43:3', 'test-plotTemporalSymmetry.R:86:3', 'test-summariseSequenceRatios.R:204:3', 'test-summariseSequenceRatios.R:413:3', 'test-summariseSequenceRatios.R:518:3', 'test-summariseSequenceRatios.R:599:3', 'test-summariseSequenceRatios.R:754:3', 'test-summariseSequenceRatios.R:792:3', 'test-summariseSequenceRatios.R:830:3', 'test-summariseSequenceRatios.R:868:3', 'test-summariseTemporalSymmetry.R:71:3', 'test-summariseTemporalSymmetry.R:96:3', 'test-tableSequenceRatios.R:46:3', 'test-tableSequenceRatios.R:70:3', 'test-tableTemporalSymmetry.R:46:3', 'test-tableTemporalSymmetry.R:70:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-generateSequenceCohortSet.R:37:3'): one ID against one ID, example 1 ── Error in `mockCohortSymmetry()`: The package "duckdb" is required. Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry() at test-generateSequenceCohortSet.R:37:3 2. └─rlang::check_installed("duckdb") ── Error ('test-generateSequenceCohortSet.R:80:3'): one ID against one ID, example 3 ── Error in `mockCohortSymmetry()`: The package "duckdb" is required. Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry() at test-generateSequenceCohortSet.R:80:3 2. └─rlang::check_installed("duckdb") ── Error ('test-plotTemporalSymmetry.R:18:3'): plot working ──────────────────── Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb' Backtrace: ▆ 1. ├─DBI::dbConnect(duckdb::duckdb(), ":memory:") at test-plotTemporalSymmetry.R:18:3 2. ├─base::loadNamespace(x) 3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL) 4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]]) 5. │ │ └─base (local) doWithOneRestart(return(expr), restart) 6. │ └─base::stop(cond) 7. └─base (local) ``(``) ── Error ('test-summariseSequenceRatios.R:33:3'): summariseSequenceRatios ────── Error in `mockCohortSymmetry(indexCohort = indexCohort, markerCohort = markerCohort)`: The package "duckdb" is required. Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry(...) at test-summariseSequenceRatios.R:33:3 2. └─rlang::check_installed("duckdb") ── Error ('test-summariseSequenceRatios.R:99:3'): summariseSequenceRatios - testing ratios and CIs, Example 1 ── Error in `mockCohortSymmetry(indexCohort = indexCohort, markerCohort = markerCohort)`: The package "duckdb" is required. Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry(...) at test-summariseSequenceRatios.R:99:3 2. └─rlang::check_installed("duckdb") ── Error ('test-summariseSequenceRatios.R:166:3'): summariseSequenceRatios - testing ratios and CIs, Example 2 ── Error in `mockCohortSymmetry(indexCohort = indexCohort, markerCohort = markerCohort)`: The package "duckdb" is required. Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry(...) at test-summariseSequenceRatios.R:166:3 2. └─rlang::check_installed("duckdb") ── Error ('test-summariseTemporalSymmetry.R:3:3'): test summariseTemporalSymmetry ── Error in `mockCohortSymmetry()`: The package "duckdb" is required. Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry() at test-summariseTemporalSymmetry.R:3:3 2. └─rlang::check_installed("duckdb") ── Error ('test-tableSequenceRatios.R:4:3'): tableSequenceRatios - gt output ─── Error in `mockCohortSymmetry()`: The package "duckdb" is required. Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry() at test-tableSequenceRatios.R:4:3 2. └─rlang::check_installed("duckdb") ── Error ('test-tableTemporalSymmetry.R:4:3'): tableTemporalSymmetry - gt output ── Error in `mockCohortSymmetry()`: The package "duckdb" is required. Backtrace: ▆ 1. └─CohortSymmetry::mockCohortSymmetry() at test-tableTemporalSymmetry.R:4:3 2. └─rlang::check_installed("duckdb") [ FAIL 9 | WARN 0 | SKIP 55 | PASS 0 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [10s/16s] ERROR Error(s) in re-building vignettes: --- re-building ‘a01_Introduction.Rmd’ using rmarkdown Quitting from a01_Introduction.Rmd:41-48 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'duckdb' --- Backtrace: ▆ 1. └─base::library(duckdb) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'a01_Introduction.Rmd' failed with diagnostics: there is no package called 'duckdb' --- failed re-building ‘a01_Introduction.Rmd’ --- re-building ‘a02_Generate_a_sequence_cohort.Rmd’ using rmarkdown 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 Quitting from a02_Generate_a_sequence_cohort.Rmd:36-50 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'duckdb' --- Backtrace: ▆ 1. └─base::library(duckdb) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'a02_Generate_a_sequence_cohort.Rmd' failed with diagnostics: there is no package called 'duckdb' --- failed re-building ‘a02_Generate_a_sequence_cohort.Rmd’ --- re-building ‘a03_Summarise_sequence_ratios.Rmd’ using rmarkdown 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 Quitting from a03_Summarise_sequence_ratios.Rmd:32-59 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'duckdb' --- Backtrace: ▆ 1. └─base::library(duckdb) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'a03_Summarise_sequence_ratios.Rmd' failed with diagnostics: there is no package called 'duckdb' --- failed re-building ‘a03_Summarise_sequence_ratios.Rmd’ --- re-building ‘a04_Visualise_sequence_ratios.Rmd’ using rmarkdown 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 Quitting from a04_Visualise_sequence_ratios.Rmd:35-71 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'duckdb' --- Backtrace: ▆ 1. └─base::library(duckdb) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'a04_Visualise_sequence_ratios.Rmd' failed with diagnostics: there is no package called 'duckdb' --- failed re-building ‘a04_Visualise_sequence_ratios.Rmd’ --- re-building ‘a05_Summarise_temporal_symmetry.Rmd’ using rmarkdown 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 Quitting from a05_Summarise_temporal_symmetry.Rmd:31-59 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'duckdb' --- Backtrace: ▆ 1. └─base::library(duckdb) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'a05_Summarise_temporal_symmetry.Rmd' failed with diagnostics: there is no package called 'duckdb' --- failed re-building ‘a05_Summarise_temporal_symmetry.Rmd’ --- re-building ‘a06_Visualise_temporal_symmetry.Rmd’ using rmarkdown 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 Quitting from a06_Visualise_temporal_symmetry.Rmd:36-72 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'duckdb' --- Backtrace: ▆ 1. └─base::library(duckdb) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'a06_Visualise_temporal_symmetry.Rmd' failed with diagnostics: there is no package called 'duckdb' --- failed re-building ‘a06_Visualise_temporal_symmetry.Rmd’ SUMMARY: processing the following files failed: ‘a01_Introduction.Rmd’ ‘a02_Generate_a_sequence_cohort.Rmd’ ‘a03_Summarise_sequence_ratios.Rmd’ ‘a04_Visualise_sequence_ratios.Rmd’ ‘a05_Summarise_temporal_symmetry.Rmd’ ‘a06_Visualise_temporal_symmetry.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/CohortSymmetry.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:09.70, 46.26 + 6.05