Last updated on 2026-09-05 07:50:27 CEST.
| Package | OK | ERROR | Other |
|---|---|---|---|
| CodelistGenerator | 12 | 1 | |
| CohortConstructor | 12 | 1 | |
| IncidencePrevalence | 12 | 1 | |
| OmopOnSpark | 13 | 1 | |
| PhenotypeR | 13 |
Current CRAN status: OK: 12, ERROR: 1
Version: 4.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [31s/38s]
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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CodelistGenerator)
Registered S3 method overwritten by 'CodelistGenerator':
method from
print.code_search omopgenerics
>
> test_check("CodelistGenerator")
Starting 2 test processes.
> test-asCodelist.R: Limiting to concept type, domains, and vocabularies of interest
> test-asCodelist.R: Getting concepts to include
> test-asCodelist.R: Adding descendants
> test-asCodelist.R: Search completed. Finishing up.
> test-asCodelist.R: v 4 candidate concepts identified
> test-asCodelist.R: Time taken: 0 minutes and 5 seconds
> test-asCodelist.R: ! No column specifying T/F for the different codes is detected
> test-asCodelist.R: ! No column specifying T/F for the different codes is detected
Saving _problems/test-buildAchillesTables-55.R
Saving _problems/test-compareCodelists-108.R
Saving _problems/test-getCandidateCodes-7.R
Saving _problems/test-mockVocabRef-2.R
> test-searchStrategy.R: Limiting to concept type, domains, and vocabularies of interest
> test-searchStrategy.R: Getting concepts to include
> test-searchStrategy.R: Adding descendants
> test-searchStrategy.R: Search completed. Finishing up.
> test-searchStrategy.R: v 5 candidate concepts identified
> test-searchStrategy.R: Time taken: 0 minutes and 0 seconds
> test-stratifyByDoseUnit.R: Limiting to concept type, domains, and vocabularies of interest
> test-stratifyByDoseUnit.R: Getting concepts to include
Saving _problems/test-stratifyByRouteCategory-5.R
> test-stratifyByDoseUnit.R: Adding descendants
> test-stratifyByDoseUnit.R: Search completed. Finishing up.
> test-stratifyByDoseUnit.R: v 2 candidate concepts identified
> test-stratifyByDoseUnit.R: Time taken: 0 minutes and 0 seconds
Saving _problems/test-subsetOnDomain-6.R
Saving _problems/test-subsetOnRouteCategory-6.R
Saving _problems/test-summariseAchillesCodeUse-66.R
> test-tidyWords.R: Symbols "-" will be ignored.
> test-tidyWords.R: `-` will be replaced by an empty space.
> test-tidyWords.R: Symbols "[", "¹", "⁸", "]", and "-" will be ignored.
> test-tidyWords.R: `-` will be replaced by an empty space.
[ FAIL 8 | WARN 0 | SKIP 53 | PASS 179 ]
══ Skipped tests (53) ══════════════════════════════════════════════════════════
• On CRAN (50): 'test-asCodelistWithDetails.R:2:3', 'test-availableATC.R:2:3',
'test-availableConceptClassIds.R:2:3', 'test-availableDomains.R:2:3',
'test-availableDoseForms.R:2:3', 'test-availableDoseUnit.R:2:3',
'test-availableDrugIngredients.R:2:3', 'test-availableRelationshipIds.R:2:3',
'test-availableRouteCategories.R:2:3', 'test-availableVocabularies.R:2:3',
'test-buildAchillesTables.R:2:3', 'test-classCodeSearch.R:3:3',
'test-codesFrom.R:2:3', 'test-codesFrom.R:118:3',
'test-compareCodelists.R:2:3', 'test-dbms.R:4:3', 'test-dbms.R:170:3',
'test-dbms.R:308:3', 'test-dbms.R:460:3', 'test-drugCodes.R:2:3',
'test-drugCodes.R:38:3', 'test-drugCodes.R:56:3', 'test-drugCodes.R:189:3',
'test-drugCodes.R:512:3', 'test-getCandidateCodes.R:441:3',
'test-getCandidateCodes.R:479:3', 'test-getMappings.R:2:3',
'test-intersectCodelists.R:2:3', 'test-intersectCodelists.R:48:3',
'test-stratifyByBrand.R:2:3', 'test-stratifyByConcept.R:2:3',
'test-subsetOnDoseUnit.R:2:3', 'test-subsetOnIngredientRange.R:2:3',
'test-subsetOnVocabulary.R:2:3', 'test-subsetToCodesInUse.R:2:3',
'test-summariseAchillesCodeUse.R:2:3', 'test-summariseCodeUse.R:2:3',
'test-summariseCodeUse.R:361:3', 'test-summariseCodeUse.R:604:3',
'test-summariseCodeUse.R:911:3', 'test-summariseCodeUse.R:937:3',
'test-summariseCodeUse.R:969:3', 'test-summariseOrphanCodes.R:2:3',
'test-tableAchillesCodeUse.R:2:3', 'test-tableCodeUse.R:2:3',
'test-tableCodeUse.R:93:3', 'test-tableOrphanCodes.R:3:3',
'test-unionCodelists.R:2:3', 'test-unionCodelists.R:47:3',
'test-vocabUtilities.R:2:3'
• Skipping (1): 'test-summariseCodeUse.R:654:3'
• Sys.getenv("CDM5_SQL_SERVER_SERVER") == "" is TRUE (1):
'test-subsetToCodesInUse.R:57:3'
• Sys.getenv("darwinDbDatabaseServer") == "" is TRUE (1):
'test-synthea_sql_server.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-buildAchillesTables.R:55:3'): test buildAchillesTables when not all tables required are present ──
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()) at test-buildAchillesTables.R:55:3
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-compareCodelists.R:108:5'): comparing two codelists- same codes found different ways ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockVocabRef(backends[[i]])`: The package "duckdb" is required.
Backtrace:
▆
1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-compareCodelists.R:108:5
2. └─rlang::check_installed("duckdb")
── Error ('test-getCandidateCodes.R:7:5'): tests with mock db ──────────────────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockVocabRef(backends[[i]])`: The package "duckdb" is required.
Backtrace:
▆
1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-getCandidateCodes.R:7:5
2. └─rlang::check_installed("duckdb")
── Error ('test-mockVocabRef.R:2:3'): mock vocab db ────────────────────────────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockVocabRef("database")`: The package "duckdb" is required.
Backtrace:
▆
1. └─CodelistGenerator::mockVocabRef("database") at test-mockVocabRef.R:2:3
2. └─rlang::check_installed("duckdb")
── Error ('test-stratifyByRouteCategory.R:5:5'): stratify by route works ───────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockVocabRef(backends[[i]])`: The package "duckdb" is required.
Backtrace:
▆
1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-stratifyByRouteCategory.R:5:5
2. └─rlang::check_installed("duckdb")
── Error ('test-subsetOnDomain.R:6:5'): subset on domain ───────────────────────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockVocabRef(backends[[i]])`: The package "duckdb" is required.
Backtrace:
▆
1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-subsetOnDomain.R:6:5
2. └─rlang::check_installed("duckdb")
── Error ('test-subsetOnRouteCategory.R:6:5'): subset on route category ────────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockVocabRef(backends[[i]])`: The package "duckdb" is required.
Backtrace:
▆
1. └─CodelistGenerator::mockVocabRef(backends[[i]]) at test-subsetOnRouteCategory.R:6:5
2. └─rlang::check_installed("duckdb")
── Error ('test-summariseAchillesCodeUse.R:66:3'): achilles code use: multipe codelists ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockVocabRef("database")`: The package "duckdb" is required.
Backtrace:
▆
1. └─CodelistGenerator::mockVocabRef("database") at test-summariseAchillesCodeUse.R:66:3
2. └─rlang::check_installed("duckdb")
[ FAIL 8 | WARN 0 | SKIP 53 | PASS 179 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 4.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘a01_GettingOmopCdmVocabularies.Rmd’ using rmarkdown
--- finished re-building ‘a01_GettingOmopCdmVocabularies.Rmd’
--- re-building ‘a02_ExploreCDMvocabulary.Rmd’ using rmarkdown
--- finished re-building ‘a02_ExploreCDMvocabulary.Rmd’
--- re-building ‘a03_TypesOfCodelist.Rmd’ using rmarkdown
--- finished re-building ‘a03_TypesOfCodelist.Rmd’
--- re-building ‘a04_GenerateCandidateCodelist.Rmd’ using rmarkdown
--- finished re-building ‘a04_GenerateCandidateCodelist.Rmd’
--- re-building ‘a05_GenerateVocabularyBasedCodelist.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 ‘a05_GenerateVocabularyBasedCodelist.Rmd’
--- re-building ‘a06_ImportExport.Rmd’ using rmarkdown
--- finished re-building ‘a06_ImportExport.Rmd’
--- re-building ‘a08_ManipulateCodelists.Rmd’ using rmarkdown
--- finished re-building ‘a08_ManipulateCodelists.Rmd’
--- re-building ‘a09_RunCodelistDiagnostics.Rmd’ using rmarkdown
--- finished re-building ‘a09_RunCodelistDiagnostics.Rmd’
--- re-building ‘a10_CodelistGeneratorBenchmark.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 a10_CodelistGeneratorBenchmark.Rmd:25-47 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'duckdb'
---
Backtrace:
▆
1. └─base::library(duckdb)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a10_CodelistGeneratorBenchmark.Rmd' failed with diagnostics:
there is no package called 'duckdb'
--- failed re-building ‘a10_CodelistGeneratorBenchmark.Rmd’
SUMMARY: processing the following file failed:
‘a10_CodelistGeneratorBenchmark.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Current CRAN status: OK: 12, ERROR: 1
Version: 0.6.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘a00_introduction.Rmd’ using rmarkdown
--- finished re-building ‘a00_introduction.Rmd’
--- re-building ‘a01_building_base_cohorts.Rmd’ using rmarkdown
Quitting from a01_building_base_cohorts.Rmd:24-34 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'duckdb'
---
Backtrace:
▆
1. └─base::library(duckdb)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a01_building_base_cohorts.Rmd' failed with diagnostics:
there is no package called 'duckdb'
--- failed re-building ‘a01_building_base_cohorts.Rmd’
--- re-building ‘a02_cohort_table_requirements.Rmd’ using rmarkdown
--- finished re-building ‘a02_cohort_table_requirements.Rmd’
--- re-building ‘a03_require_demographics.Rmd’ using rmarkdown
--- finished re-building ‘a03_require_demographics.Rmd’
--- re-building ‘a04_require_intersections.Rmd’ using rmarkdown
--- finished re-building ‘a04_require_intersections.Rmd’
--- re-building ‘a05_update_cohort_start_end.Rmd’ using rmarkdown
--- finished re-building ‘a05_update_cohort_start_end.Rmd’
--- re-building ‘a06_concatanate_cohorts.Rmd’ using rmarkdown
--- finished re-building ‘a06_concatanate_cohorts.Rmd’
--- re-building ‘a07_filter_cohorts.Rmd’ using rmarkdown
--- finished re-building ‘a07_filter_cohorts.Rmd’
--- re-building ‘a08_split_cohorts.Rmd’ using rmarkdown
--- finished re-building ‘a08_split_cohorts.Rmd’
--- re-building ‘a09_combine_cohorts.Rmd’ using rmarkdown
--- finished re-building ‘a09_combine_cohorts.Rmd’
--- re-building ‘a10_match_cohorts.Rmd’ using rmarkdown
--- finished re-building ‘a10_match_cohorts.Rmd’
--- re-building ‘a11_benchmark.Rmd’ using rmarkdown
--- finished re-building ‘a11_benchmark.Rmd’
--- re-building ‘a12_behind_the_scenes.Rmd’ using rmarkdown
--- finished re-building ‘a12_behind_the_scenes.Rmd’
SUMMARY: processing the following file failed:
‘a01_building_base_cohorts.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Current CRAN status: OK: 12, ERROR: 1
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [21s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(IncidencePrevalence)
>
> test_check("IncidencePrevalence")
Starting 2 test processes.
Saving _problems/test-estimatePrevalence-3.R
Saving _problems/test-estimatePrevalence-1221.R
Saving _problems/test-estimatePrevalence-1269.R
Saving _problems/test-estimateIncidence-2.R
Saving _problems/test-estimateIncidence-1022.R
Saving _problems/test-generateDenominatorCohortSet-2.R
Saving _problems/test-generateDenominatorCohortSet-71.R
Saving _problems/test-generateDenominatorCohortSet-2455.R
[ FAIL 8 | WARN 0 | SKIP 101 | PASS 0 ]
══ Skipped tests (101) ═════════════════════════════════════════════════════════
• On CRAN (101): 'test-dateUtilities.R:2:3',
'test-benchmarkIncidencePrevalence.R:2:3',
'test-benchmarkIncidencePrevalence.R:45:3', 'test-estimatePrevalence.R:41:3',
'test-estimatePrevalence.R:93:3', 'test-estimatePrevalence.R:150:3',
'test-estimatePrevalence.R:269:3', 'test-estimatePrevalence.R:413:3',
'test-estimatePrevalence.R:495:3', 'test-estimatePrevalence.R:646:3',
'test-estimatePrevalence.R:697:3', 'test-estimatePrevalence.R:742:3',
'test-estimatePrevalence.R:797:3', 'test-estimatePrevalence.R:845:3',
'test-estimatePrevalence.R:869:3', 'test-estimatePrevalence.R:894:3',
'test-estimatePrevalence.R:1035:3', 'test-estimatePrevalence.R:1082:3',
'test-estimatePrevalence.R:1115:3', 'test-estimatePrevalence.R:1194:3',
'test-estimatePrevalence.R:1246:3', 'test-estimatePrevalence.R:1416:3',
'test-estimatePrevalence.R:1458:3', 'test-estimatePrevalence.R:1504:3',
'test-estimatePrevalence.R:1556:3', 'test-estimatePrevalence.R:1672:3',
'test-estimateIncidence.R:57:3', 'test-estimateIncidence.R:120:3',
'test-estimateIncidence.R:230:3', 'test-estimateIncidence.R:300:3',
'test-estimateIncidence.R:399:3', 'test-estimateIncidence.R:503:3',
'test-estimateIncidence.R:598:3', 'test-estimateIncidence.R:762:3',
'test-estimateIncidence.R:869:3', 'test-estimateIncidence.R:1063:3',
'test-estimateIncidence.R:1127:3', 'test-estimateIncidence.R:1184:3',
'test-estimateIncidence.R:1269:3', 'test-estimateIncidence.R:1413:3',
'test-estimateIncidence.R:1529:3', 'test-estimateIncidence.R:1608:3',
'test-estimateIncidence.R:1716:3', 'test-estimateIncidence.R:1820:3',
'test-estimateIncidence.R:1979:3', 'test-estimateIncidence.R:2035:3',
'test-estimateIncidence.R:2233:3', 'test-estimateIncidence.R:2432:3',
'test-estimateIncidence.R:2517:3', 'test-estimateIncidence.R:2943:3',
'test-estimateIncidence.R:2991:3', 'test-estimateIncidence.R:3046:3',
'test-estimateIncidence.R:3104:3', 'test-estimateIncidence.R:3127:3',
'test-estimateIncidence.R:3142:3', 'test-estimateIncidence.R:3182:3',
'test-estimateIncidence.R:3344:3', 'test-estimateIncidence.R:3423:3',
'test-estimateIncidence.R:3467:3', 'test-estimateIncidence.R:3513:3',
'test-estimateIncidence.R:3561:3', 'test-getStudyDays.R:2:3',
'test-getStudyDays.R:238:3', 'test-mockIncidencePrevalence.R:2:3',
'test-mockIncidencePrevalence.R:39:3', 'test-mockIncidencePrevalence.R:69:3',
'test-mockIncidencePrevalence.R:171:3',
'test-generateDenominatorCohortSet.R:138:3',
'test-generateDenominatorCohortSet.R:185:3',
'test-generateDenominatorCohortSet.R:289:3',
'test-generateDenominatorCohortSet.R:326:3',
'test-generateDenominatorCohortSet.R:591:3',
'test-generateDenominatorCohortSet.R:641:3',
'test-generateDenominatorCohortSet.R:720:3',
'test-generateDenominatorCohortSet.R:812:3',
'test-generateDenominatorCohortSet.R:855:3',
'test-generateDenominatorCohortSet.R:907:3',
'test-generateDenominatorCohortSet.R:991:3',
'test-generateDenominatorCohortSet.R:1118:3',
'test-generateDenominatorCohortSet.R:1199:3',
'test-generateDenominatorCohortSet.R:1263:3',
'test-generateDenominatorCohortSet.R:1316:3',
'test-generateDenominatorCohortSet.R:1374:3',
'test-generateDenominatorCohortSet.R:1449:3',
'test-generateDenominatorCohortSet.R:1572:3',
'test-generateDenominatorCohortSet.R:1673:3',
'test-generateDenominatorCohortSet.R:1726:3',
'test-generateDenominatorCohortSet.R:1789:3',
'test-generateDenominatorCohortSet.R:2018:3',
'test-generateDenominatorCohortSet.R:2109:3',
'test-generateDenominatorCohortSet.R:2309:3',
'test-generateDenominatorCohortSet.R:2413:3', 'test-tables.R:2:3',
'test-tables.R:126:3', 'test-plotting.R:2:3', 'test-plotting.R:203:3',
'test-plotting.R:252:3', 'test-plotting.R:302:3', 'test-plotting.R:366:3',
'test-tidyResults.R:2:3', 'test-tidyResults.R:57:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-estimatePrevalence.R:2:3'): mock db: check output format ───────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence()`: The package "duckdb" is required.
Backtrace:
▆
1. ├─mockIncidencePrevalence() %>% ... at test-estimatePrevalence.R:2:3
2. ├─IncidencePrevalence::generateDenominatorCohortSet(., name = "denominator")
3. │ └─IncidencePrevalence:::fetchDenominatorCohortSet(...)
4. │ └─IncidencePrevalence:::checkInputGenerateDCS(...)
5. │ └─omopgenerics::validateCdmArgument(cdm)
6. │ └─omopgenerics::assertClass(...)
7. │ ├─omopgenerics:::checkEmpty(...)
8. │ ├─omopgenerics:::checkClass(...)
9. │ ├─omopgenerics:::checkLength(...)
10. │ ├─omopgenerics:::checkNull(createCheckObject(x), null)
11. │ └─omopgenerics:::createCheckObject(x)
12. └─IncidencePrevalence::mockIncidencePrevalence()
13. └─rlang::check_installed("duckdb")
── Error ('test-estimatePrevalence.R:1221:3'): mock db: if missing cohort attributes ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence()`: The package "duckdb" is required.
Backtrace:
▆
1. └─IncidencePrevalence::mockIncidencePrevalence() at test-estimatePrevalence.R:1221:3
2. └─rlang::check_installed("duckdb")
── Error ('test-estimatePrevalence.R:1266:3'): mock db: prevalence using strata vars ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence(sampleSize = 1000, outPre = 0.7)`: The package "duckdb" is required.
Backtrace:
▆
1. └─IncidencePrevalence::mockIncidencePrevalence(...) at test-estimatePrevalence.R:1266:3
2. └─rlang::check_installed("duckdb")
── Error ('test-estimateIncidence.R:2:3'): mock db: check output format ────────
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence()`: The package "duckdb" is required.
Backtrace:
▆
1. └─IncidencePrevalence::mockIncidencePrevalence() at test-estimateIncidence.R:2:3
2. └─rlang::check_installed("duckdb")
── Error ('test-estimateIncidence.R:1020:3'): mock db: multiple denominator inputs ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence(sampleSize = 6000, maxOutcomeDays = 5, maxOutcomes = 6)`: The package "duckdb" is required.
Backtrace:
▆
1. └─IncidencePrevalence::mockIncidencePrevalence(...) at test-estimateIncidence.R:1020:3
2. └─rlang::check_installed("duckdb")
── Error ('test-generateDenominatorCohortSet.R:2:3'): mock db: check output format ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence()`: The package "duckdb" is required.
Backtrace:
▆
1. └─IncidencePrevalence::mockIncidencePrevalence() at test-generateDenominatorCohortSet.R:2:3
2. └─rlang::check_installed("duckdb")
── Error ('test-generateDenominatorCohortSet.R:68:3'): mock db: checks on working example ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence(personTable = personTable, observationPeriodTable = observationPeriodTable)`: The package "duckdb" is required.
Backtrace:
▆
1. └─IncidencePrevalence::mockIncidencePrevalence(...) at test-generateDenominatorCohortSet.R:68:3
2. └─rlang::check_installed("duckdb")
── Error ('test-generateDenominatorCohortSet.R:2455:3'): mock db: target cohort extra columns ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `mockIncidencePrevalence()`: The package "duckdb" is required.
Backtrace:
▆
1. └─IncidencePrevalence::mockIncidencePrevalence() at test-generateDenominatorCohortSet.R:2455:3
2. └─rlang::check_installed("duckdb")
[ FAIL 8 | WARN 0 | SKIP 101 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’ using rmarkdown
Quitting from a01_Introduction_to_IncidencePrevalence.Rmd:42-47 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `mockIncidencePrevalence()`:
! The package "duckdb" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a01_Introduction_to_IncidencePrevalence.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’
--- re-building ‘a02_Creating_denominator_populations.Rmd’ using rmarkdown
Quitting from a02_Creating_denominator_populations.Rmd:82-84 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `mockIncidencePrevalence()`:
! The package "duckdb" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a02_Creating_denominator_populations.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building ‘a02_Creating_denominator_populations.Rmd’
--- re-building ‘a03_Creating_target_denominator_populations.Rmd’ using rmarkdown
Quitting from a03_Creating_target_denominator_populations.Rmd:33-85 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `mockIncidencePrevalence()`:
! The package "duckdb" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a03_Creating_target_denominator_populations.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building ‘a03_Creating_target_denominator_populations.Rmd’
--- re-building ‘a04_Calculating_prevalence.Rmd’ using rmarkdown
Quitting from a04_Calculating_prevalence.Rmd:47-71 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `mockIncidencePrevalence()`:
! The package "duckdb" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a04_Calculating_prevalence.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building ‘a04_Calculating_prevalence.Rmd’
--- re-building ‘a05_Calculating_incidence.Rmd’ using rmarkdown
Quitting from a05_Calculating_incidence.Rmd:76-100 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `mockIncidencePrevalence()`:
! The package "duckdb" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a05_Calculating_incidence.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building ‘a05_Calculating_incidence.Rmd’
--- re-building ‘a06_Working_with_IncidencePrevalence_Results.Rmd’ using rmarkdown
Quitting from a06_Working_with_IncidencePrevalence_Results.Rmd:30-70 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `mockIncidencePrevalence()`:
! The package "duckdb" is required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'a06_Working_with_IncidencePrevalence_Results.Rmd' failed with diagnostics:
The package "duckdb" is required.
--- failed re-building ‘a06_Working_with_IncidencePrevalence_Results.Rmd’
--- re-building ‘a07_benchmark.Rmd’ using rmarkdown
--- finished re-building ‘a07_benchmark.Rmd’
SUMMARY: processing the following files failed:
‘a01_Introduction_to_IncidencePrevalence.Rmd’
‘a02_Creating_denominator_populations.Rmd’
‘a03_Creating_target_denominator_populations.Rmd’
‘a04_Calculating_prevalence.Rmd’ ‘a05_Calculating_incidence.Rmd’
‘a06_Working_with_IncidencePrevalence_Results.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Current CRAN status: OK: 13, Other: 1
Current CRAN status: OK: 13