Last updated on 2025-12-28 01:49:08 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| CodelistGenerator | 1 | 12 | |
| CohortConstructor | 1 | 12 | |
| IncidencePrevalence | 13 | ||
| OmopOnSpark | 13 | ||
| PhenotypeR | 9 | 2 | 2 |
Current CRAN status: ERROR: 1, OK: 12
Version: 4.0.0
Check: package dependencies
Result: ERROR
Package required and available but unsuitable version: ‘PatientProfiles’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64
Current CRAN status: ERROR: 1, OK: 12
Version: 0.6.1
Check: package dependencies
Result: ERROR
Packages required and available but unsuitable versions:
'PatientProfiles', 'CodelistGenerator'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 9, NOTE: 2, OK: 2
Version: 0.2.0
Check: dependencies in R code
Result: WARN
Missing or unexported object: ‘CodelistGenerator::buildAchillesTables’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [24s/27s]
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")
* 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$my_cohort) at test-codelistDiagnostics.R:90:3
2. └─MeasurementDiagnostics::summariseCohortMeasurementUse(...)
3. └─MeasurementDiagnostics:::summariseMeasurementUseInternal(...)
4. └─omopgenerics::assertChoice(checks, choices = allowedChecks)
5. └─omopgenerics:::errorMessage(...)
6. └─cli::cli_abort(message = message, call = call)
7. └─rlang::abort(...)
[ FAIL 1 | WARN 4 | SKIP 21 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘CodelistDiagnostics.Rmd’ using rmarkdown
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip'
Content type 'application/zip' length 593048982 bytes (565.6 MB)
==================================================
downloaded 565.6 MB
Quitting from CodelistDiagnostics.Rmd:60-62 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `summariseMeasurementUseInternal()`:
✖ `checks` a choice between: measurement_summary,
measurement_value_as_number, and measurement_value_as_concept.
! `checks` must be a choice between: measurement_summary,
measurement_value_as_number, and measurement_value_as_concept; it can not
contain NA; it can not be NULL.
---
Backtrace:
▆
1. └─PhenotypeR::codelistDiagnostics(cdm$injuries)
2. └─MeasurementDiagnostics::summariseCohortMeasurementUse(...)
3. └─MeasurementDiagnostics:::summariseMeasurementUseInternal(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/15s]
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")
* 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-debian-gcc
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [22s/23s]
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")
* 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]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `summariseMeasurementUseInternal()`:
✖ `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$injuries)
2. └─MeasurementDiagnostics::summariseCohortMeasurementUse(...)
3. └─MeasurementDiagnostics:::summariseMeasurementUseInternal(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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’ [19s/21s]
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")
* 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: tests
Result: ERROR
Running 'testthat.R' [18s]
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")
* 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$my_cohort) at test-codelistDiagnostics.R:90:3
2. └─MeasurementDiagnostics::summariseCohortMeasurementUse(...)
3. └─MeasurementDiagnostics:::summariseMeasurementUseInternal(...)
4. └─omopgenerics::assertChoice(checks, choices = allowedChecks)
5. └─omopgenerics:::errorMessage(...)
6. └─cli::cli_abort(message = message, call = call)
7. └─rlang::abort(...)
[ FAIL 1 | WARN 4 | SKIP 21 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'CodelistDiagnostics.Rmd' using rmarkdown
trying URL 'https://cdmconnectordata.blob.core.windows.net/cdmconnector-example-data/synpuf-1k_5.3.zip'
Content type 'application/zip' length 593048982 bytes (565.6 MB)
==================================================
downloaded 565.6 MB
Quitting from CodelistDiagnostics.Rmd:60-62 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `summariseMeasurementUseInternal()`:
✖ `checks` a choice between: measurement_summary,
measurement_value_as_number, and measurement_value_as_concept.
! `checks` must be a choice between: measurement_summary,
measurement_value_as_number, and measurement_value_as_concept; it can not
contain NA; it can not be NULL.
---
Backtrace:
▆
1. └─PhenotypeR::codelistDiagnostics(cdm$injuries)
2. └─MeasurementDiagnostics::summariseCohortMeasurementUse(...)
3. └─MeasurementDiagnostics:::summariseMeasurementUseInternal(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
--- 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
--- 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
--- finished re-building 'PhenotypeDiagnostics.Rmd'
--- re-building 'PhenotypeExpectations.Rmd' using rmarkdown
--- 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
--- finished re-building 'PopulationDiagnostics.Rmd'
--- re-building 'ShinyDiagnostics.Rmd' using rmarkdown
--- finished re-building 'ShinyDiagnostics.Rmd'
SUMMARY: processing the following file failed:
'CodelistDiagnostics.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [22s/32s]
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")
* 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-patched-linux-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [22s/25s]
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")
========================>------ 79% | ETA: 1s
* 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-release-linux-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running 'testthat.R' [17s]
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")
* 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-release-windows-x86_64
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
Version: 0.2.0
Check: tests
Result: ERROR
Running 'testthat.R' [25s]
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")
============================>-- 93% | ETA: 0s
* 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-oldrel-windows-x86_64
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