Last updated on 2025-12-18 05:50:06 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 5.58 | 593.05 | 598.63 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 3.77 | 425.19 | 428.96 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 9.00 | 705.81 | 714.81 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 9.00 | 666.52 | 675.52 | ERROR | |
| r-devel-windows-x86_64 | 0.2.0 | 8.00 | 508.00 | 516.00 | OK | |
| r-patched-linux-x86_64 | 0.2.0 | 5.55 | 568.89 | 574.44 | OK | |
| r-release-linux-x86_64 | 0.2.0 | 4.13 | 567.98 | 572.11 | OK | |
| r-release-macos-arm64 | 0.2.0 | OK | ||||
| r-release-macos-x86_64 | 0.2.0 | 3.00 | 400.00 | 403.00 | OK | |
| r-release-windows-x86_64 | 0.2.0 | 7.00 | 518.00 | 525.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.0 | NOTE | ||||
| r-oldrel-macos-x86_64 | 0.2.0 | 3.00 | 409.00 | 412.00 | NOTE | |
| r-oldrel-windows-x86_64 | 0.2.0 | 10.00 | 716.00 | 726.00 | NOTE |
Version: 0.2.0
Check: dependencies in R code
Result: WARN
Missing or unexported object: ‘CodelistGenerator::buildAchillesTables’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [39s/118s]
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(PhenotypeR)
>
> test_check("PhenotypeR")
=========>--------------------- 29% | ETA: 10s
==========================>---- 86% | ETA: 2s
* Getting codelists from cohorts
* Getting index event breakdown
Getting counts of b codes for cohort cohort_1
* Getting diagnostics for measurement concepts
Saving _problems/test-codelistDiagnostics-90.R
[ FAIL 1 | WARN 4 | SKIP 21 | PASS 0 ]
══ Skipped tests (21) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-addCodelistAttribute.R:2:3',
'test-addCodelistAttribute.R:70:3', 'test-addCodelistAttribute.R:118:3',
'test-codelistDiagnostics.R:2:3', 'test-codelistDiagnostics.R:48:3',
'test-cohortDiagnostics.R:2:3', 'test-cohortDiagnostics.R:51:3',
'test-databaseDiagnostics.R:2:3', 'test-dbms.R:3:3', 'test-dbms.R:25:3',
'test-getCohortExpectations.R:3:3', 'test-getCohortExpectations.R:26:3',
'test-getCohortExpectations.R:61:3', 'test-phenotypeDiagnostics.R:3:3',
'test-populationDiagnostics.R:2:3', 'test-shinyDiagnostics.R:3:3',
'test-shinyDiagnostics.R:53:3'
• empty test (4): 'test-cohortDiagnostics.R:144:1',
'test-cohortDiagnostics.R:148:1', 'test-cohortDiagnostics.R:152:1',
'test-cohortDiagnostics.R:158:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-codelistDiagnostics.R:90:3'): measurementDiagnostics working ───
Error in `summariseMeasurementUseInternal(cdm = cdm, codes = codes, cohort = cohort, timing = timing, timingName = timing, byConcept = byConcept, byYear = byYear, bySex = bySex, ageGroup = ageGroup, dateRange = dateRange, estimates = estimates, histogram = histogram, checks = checks)`: x `checks` a choice between: measurement_summary, measurement_value_as_number, and measurement_value_as_concept.
! `checks` must be a choice between: measurement_summary, measurement_value_as_number, and measurement_value_as_concept; it can not contain NA; it can not be NULL.
Backtrace:
▆
1. └─PhenotypeR::codelistDiagnostics(cdm$my_cohort) at test-codelistDiagnostics.R:90:3
2. └─MeasurementDiagnostics::summariseCohortMeasurementUse(...)
3. └─MeasurementDiagnostics:::summariseMeasurementUseInternal(...)
4. └─omopgenerics::assertChoice(checks, choices = allowedChecks)
5. └─omopgenerics:::errorMessage(...)
6. └─cli::cli_abort(message = message, call = call)
7. └─rlang::abort(...)
[ FAIL 1 | WARN 4 | SKIP 21 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘CodelistDiagnostics.Rmd’ using rmarkdown
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip'
Content type 'application/zip' length 593048982 bytes (565.6 MB)
==================================================
downloaded 565.6 MB
Quitting from CodelistDiagnostics.Rmd:60-62 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'CodelistDiagnostics.Rmd' failed with diagnostics:
✖ `checks` a choice between: measurement_summary,
measurement_value_as_number, and measurement_value_as_concept.
! `checks` must be a choice between: measurement_summary,
measurement_value_as_number, and measurement_value_as_concept; it can not
contain NA; it can not be NULL.
--- failed re-building ‘CodelistDiagnostics.Rmd’
--- re-building ‘CohortDiagnostics.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘CohortDiagnostics.Rmd’
--- re-building ‘DatabaseDiagnostics.Rmd’ using rmarkdown
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip'
Content type 'application/zip' length 593048982 bytes (565.6 MB)
==================================================
downloaded 565.6 MB
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘DatabaseDiagnostics.Rmd’
--- re-building ‘PhenotypeDiagnostics.Rmd’ using rmarkdown
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip'
Content type 'application/zip' length 593048982 bytes (565.6 MB)
==================================================
downloaded 565.6 MB
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘PhenotypeDiagnostics.Rmd’
--- re-building ‘PhenotypeExpectations.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘PhenotypeExpectations.Rmd’
--- re-building ‘PopulationDiagnostics.Rmd’ using rmarkdown
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip'
Content type 'application/zip' length 593048982 bytes (565.6 MB)
==================================================
downloaded 565.6 MB
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘PopulationDiagnostics.Rmd’
--- re-building ‘ShinyDiagnostics.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘ShinyDiagnostics.Rmd’
SUMMARY: processing the following file failed:
‘CodelistDiagnostics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [36s/62s]
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(PhenotypeR)
>
> test_check("PhenotypeR")
===============>--------------- 50% | ETA: 2s
* Getting codelists from cohorts
* Getting index event breakdown
Getting counts of b codes for cohort cohort_1
* Getting diagnostics for measurement concepts
Saving _problems/test-codelistDiagnostics-90.R
[ FAIL 1 | WARN 4 | SKIP 21 | PASS 0 ]
══ Skipped tests (21) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-addCodelistAttribute.R:2:3',
'test-addCodelistAttribute.R:70:3', 'test-addCodelistAttribute.R:118:3',
'test-codelistDiagnostics.R:2:3', 'test-codelistDiagnostics.R:48:3',
'test-cohortDiagnostics.R:2:3', 'test-cohortDiagnostics.R:51:3',
'test-databaseDiagnostics.R:2:3', 'test-dbms.R:3:3', 'test-dbms.R:25:3',
'test-getCohortExpectations.R:3:3', 'test-getCohortExpectations.R:26:3',
'test-getCohortExpectations.R:61:3', 'test-phenotypeDiagnostics.R:3:3',
'test-populationDiagnostics.R:2:3', 'test-shinyDiagnostics.R:3:3',
'test-shinyDiagnostics.R:53:3'
• empty test (4): 'test-cohortDiagnostics.R:144:1',
'test-cohortDiagnostics.R:148:1', 'test-cohortDiagnostics.R:152:1',
'test-cohortDiagnostics.R:158:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-codelistDiagnostics.R:90:3'): measurementDiagnostics working ───
Error in `summariseMeasurementUseInternal(cdm = cdm, codes = codes, cohort = cohort, timing = timing, timingName = timing, byConcept = byConcept, byYear = byYear, bySex = bySex, ageGroup = ageGroup, dateRange = dateRange, estimates = estimates, histogram = histogram, checks = checks)`: x `checks` a choice between: measurement_summary, measurement_value_as_number, and measurement_value_as_concept.
! `checks` must be a choice between: measurement_summary, measurement_value_as_number, and measurement_value_as_concept; it can not contain NA; it can not be NULL.
Backtrace:
▆
1. └─PhenotypeR::codelistDiagnostics(cdm$my_cohort) at test-codelistDiagnostics.R:90:3
2. └─MeasurementDiagnostics::summariseCohortMeasurementUse(...)
3. └─MeasurementDiagnostics:::summariseMeasurementUseInternal(...)
4. └─omopgenerics::assertChoice(checks, choices = allowedChecks)
5. └─omopgenerics:::errorMessage(...)
6. └─cli::cli_abort(message = message, call = call)
7. └─rlang::abort(...)
[ FAIL 1 | WARN 4 | SKIP 21 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2.0
Check: installed package size
Result: NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
doc 4.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64