Last updated on 2026-05-13 01:49:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.4 | 5.11 | 636.32 | 641.43 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.4 | 3.04 | 50.16 | 53.20 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.4 | 8.00 | 992.34 | 1000.34 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.4 | 9.00 | 1065.28 | 1074.28 | OK | |
| r-devel-windows-x86_64 | 0.2.4 | 8.00 | 512.00 | 520.00 | OK | |
| r-patched-linux-x86_64 | 0.2.4 | 4.20 | 604.44 | 608.64 | OK | |
| r-release-linux-x86_64 | 0.2.4 | 5.13 | 599.97 | 605.10 | OK | |
| r-release-macos-arm64 | 0.2.4 | 1.00 | 153.00 | 154.00 | OK | |
| r-release-macos-x86_64 | 0.2.4 | 4.00 | 708.00 | 712.00 | OK | |
| r-release-windows-x86_64 | 0.2.4 | 10.00 | 502.00 | 512.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.4 | OK | ||||
| r-oldrel-macos-x86_64 | 0.2.4 | 3.00 | 342.00 | 345.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.4 | 9.00 | 740.00 | 749.00 | OK |
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [8s/9s]
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-debian-gcc
Version: 0.2.4
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-debian-gcc