CRAN Package Check Results for Package CohortSymmetry

Last updated on 2026-09-21 17:50:46 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.3.0	4.89	564.08	568.97	OK
r-devel-linux-x86_64-debian-gcc	0.3.0	3.34	426.42	429.76	OK
r-devel-linux-x86_64-fedora-clang	0.3.0			54.52	ERROR
r-devel-linux-x86_64-fedora-gcc	0.3.0			376.77	OK
r-devel-windows-x86_64	0.3.0	9.00	486.00	495.00	OK
r-patched-linux-x86_64	0.3.0	4.80	550.95	555.75	OK
r-release-linux-x86_64	0.3.0	4.97	548.91	553.88	OK
r-release-macos-arm64	0.3.0	1.00	147.00	148.00	OK
r-release-macos-x86_64	0.3.0	4.00	459.00	463.00	OK
r-release-windows-x86_64	0.3.0	7.00	461.00	468.00	OK
r-oldrel-macos-arm64	0.3.0	1.00	235.00	236.00	OK
r-oldrel-macos-x86_64	0.3.0	3.00	429.00	432.00	OK
r-oldrel-windows-x86_64	0.3.0	9.00	701.00	710.00	OK

Check Details

Version: 0.3.0
Check: tests
Result: 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/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 ── <rlib_error_package_not_found/rlang_error/error/condition> 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 ── <rlib_error_package_not_found/rlang_error/error/condition> 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) `<fn>`(`<pckgNtFE>`) ── Error ('test-summariseSequenceRatios.R:33:3'): summariseSequenceRatios ────── <rlib_error_package_not_found/rlang_error/error/condition> 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 ── <rlib_error_package_not_found/rlang_error/error/condition> 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 ── <rlib_error_package_not_found/rlang_error/error/condition> 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 ── <rlib_error_package_not_found/rlang_error/error/condition> 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 ─── <rlib_error_package_not_found/rlang_error/error/condition> 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 ── <rlib_error_package_not_found/rlang_error/error/condition> 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 Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.3.0
Check: re-building of vignette outputs
Result: 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/rlang_error> 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/rlang_error> 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/rlang_error> 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/rlang_error> 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/rlang_error> 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/rlang_error> 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 Flavor: r-devel-linux-x86_64-fedora-clang