Last updated on 2024-01-14 04:57:51 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.1 | 6.44 | 335.28 | 341.72 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.1.1 | 4.72 | 243.72 | 248.44 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.1.1 | 327.09 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.1.1 | 404.00 | OK | |||
| r-devel-windows-x86_64 | 2.1.1 | 7.00 | 240.00 | 247.00 | OK | |
| r-patched-linux-x86_64 | 2.1.1 | 4.67 | 323.33 | 328.00 | OK | |
| r-release-linux-x86_64 | 2.1.1 | 4.46 | 319.89 | 324.35 | OK | |
| r-release-macos-arm64 | 2.1.1 | 115.00 | OK | |||
| r-release-macos-x86_64 | 2.1.1 | 373.00 | OK | |||
| r-release-windows-x86_64 | 2.1.1 | 9.00 | 318.00 | 327.00 | OK | |
| r-oldrel-macos-arm64 | 2.1.1 | 117.00 | OK | |||
| r-oldrel-windows-x86_64 | 2.1.1 | 8.00 | 317.00 | 325.00 | OK |
Version: 2.1.1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘arrow’
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [176s/230s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(CodelistGenerator)
>
> test_check("CodelistGenerator")
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding descendants
v 3 candidate concepts identified
Time taken: 0 minutes and 4 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding descendants
v 2 candidate concepts identified
Time taken: 0 minutes and 3 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding descendants
v 3 candidate concepts identified
Time taken: 0 minutes and 4 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding concepts using synonymns
condition domain: Adding descendants
v 4 candidate concepts identified
Time taken: 0 minutes and 5 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
v 1 candidate concept identified
Time taken: 0 minutes and 3 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
v 2 candidate concepts identified
Time taken: 0 minutes and 3 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding descendants
v 5 candidate concepts identified
Time taken: 0 minutes and 3 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding descendants
condition domain: Adding ancestor
v 4 candidate concepts identified
Time taken: 0 minutes and 4 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding descendants
condition domain: Adding ancestor
v 2 candidate concepts identified
Time taken: 0 minutes and 3 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding descendants
v 5 candidate concepts identified
Time taken: 0 minutes and 3 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding concepts using synonymns
condition domain: Adding descendants
v 4 candidate concepts identified
Time taken: 0 minutes and 4 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding descendants
v 2 candidate concepts identified
Time taken: 0 minutes and 3 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding codes from non-standard
v 2 candidate concepts identified
Time taken: 0 minutes and 5 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding codes from non-standard
v 1 candidate concept identified
Time taken: 0 minutes and 5 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding concepts using synonymns
condition domain: Adding descendants
condition domain: Adding ancestor
condition domain: Adding codes from non-standard
v 5 candidate concepts identified
Time taken: 0 minutes and 6 seconds
drug domain: Limiting to domains of interest
drug: Getting concepts to include
drug domain: Adding concepts using synonymns
drug domain: Adding ancestor
v 1 candidate concept identified
Time taken: 0 minutes and 10 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding concepts using synonymns
condition domain: Adding descendants
condition domain: Adding ancestor
drug domain: Limiting to domains of interest
drug: Getting concepts to include
drug domain: Adding concepts using synonymns
drug domain: Adding descendants
drug domain: Adding ancestor
v 7 candidate concepts identified
Time taken: 0 minutes and 16 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
No codes found for the given search strategy
Time taken: 0 minutes and 4 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
v 1 candidate concept identified
Time taken: 0 minutes and 4 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
No codes found for the given search strategy
Time taken: 0 minutes and 4 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding descendants
some other table domain: Limiting to domains of interest
some other table: Getting concepts to include
v 3 candidate concepts identified
Time taken: 0 minutes and 8 seconds
some other table domain: Limiting to domains of interest
some other table: Getting concepts to include
No codes found for the given search strategy
Time taken: 0 minutes and 5 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
observation domain: Limiting to domains of interest
observation: Getting concepts to include
v 4 candidate concepts identified
Time taken: 0 minutes and 8 seconds
condition domain: Limiting to domains of interest
condition: Getting concepts to include
observation domain: Limiting to domains of interest
observation: Getting concepts to include
v 1 candidate concept identified
Time taken: 0 minutes and 9 seconds
-- No codes found --
i No ICD-10 chapter codes were found in the concept table.
-- Were ICD-10 codes included when loading vocabularies into the database?
-- No codes found --
i No ICD-10 chapter codes were found in the concept table.
-- Were ICD-10 codes included when loading vocabularies into the database?
condition domain: Limiting to domains of interest
condition: Getting concepts to include
condition domain: Adding descendants
v 5 candidate concepts identified
Time taken: 0 minutes and 3 seconds
[ FAIL 9 | WARN 0 | SKIP 5 | PASS 129 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-summariseCodeUse.R:2:1', 'test-summariseCodeUse.R:290:3'
• Sys.getenv("CDM5_REDSHIFT_DBNAME") == "" is TRUE (2):
'test-codesFrom.R:100:3', 'test-summariseCodeUse.R:498:3'
• Sys.getenv("darwinDbDatabaseServer") == "" is TRUE (1):
'test-synthea_sql_server.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-codesFrom.R:6:5'): test inputs - mock ──────────────────────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1.
i With name: cdm_source.
Caused by error in `loadNamespace()`:
! there is no package called 'arrow'
Backtrace:
▆
1. ├─CodelistGenerator::mockVocabRef(backends[[i]]) at test-codesFrom.R:6:5
2. │ └─CDMConnector::stow(cdm, dOut)
3. │ └─purrr::walk2(...)
4. │ └─purrr::map2(.x, .y, .f, ..., .progress = .progress)
5. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
6. │ ├─purrr:::with_indexed_errors(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ ├─purrr:::call_with_cleanup(...)
9. │ └─CDMConnector (local) .f(.x[[i]], .y[[i]], ...)
10. ├─base::loadNamespace(x)
11. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
12. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
13. │ │ └─base (local) doWithOneRestart(return(expr), restart)
14. │ └─base::stop(cond)
15. └─purrr (local) `<fn>`(`<pckgNtFE>`)
16. └─cli::cli_abort(...)
17. └─rlang::abort(...)
── Error ('test-drugCodes.R:5:3'): getATCCodes working ─────────────────────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1.
i With name: cdm_source.
Caused by error in `loadNamespace()`:
! there is no package called 'arrow'
Backtrace:
▆
1. ├─CodelistGenerator::mockVocabRef(backend = backends[i]) at test-drugCodes.R:5:3
2. │ └─CDMConnector::stow(cdm, dOut)
3. │ └─purrr::walk2(...)
4. │ └─purrr::map2(.x, .y, .f, ..., .progress = .progress)
5. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
6. │ ├─purrr:::with_indexed_errors(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ ├─purrr:::call_with_cleanup(...)
9. │ └─CDMConnector (local) .f(.x[[i]], .y[[i]], ...)
10. ├─base::loadNamespace(x)
11. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
12. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
13. │ │ └─base (local) doWithOneRestart(return(expr), restart)
14. │ └─base::stop(cond)
15. └─purrr (local) `<fn>`(`<pckgNtFE>`)
16. └─cli::cli_abort(...)
17. └─rlang::abort(...)
── Error ('test-drugCodes.R:33:5'): getATCCodes expected errors ────────────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1.
i With name: cdm_source.
Caused by error in `loadNamespace()`:
! there is no package called 'arrow'
Backtrace:
▆
1. ├─CodelistGenerator::mockVocabRef(backend = backends[i]) at test-drugCodes.R:33:5
2. │ └─CDMConnector::stow(cdm, dOut)
3. │ └─purrr::walk2(...)
4. │ └─purrr::map2(.x, .y, .f, ..., .progress = .progress)
5. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
6. │ ├─purrr:::with_indexed_errors(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ ├─purrr:::call_with_cleanup(...)
9. │ └─CDMConnector (local) .f(.x[[i]], .y[[i]], ...)
10. ├─base::loadNamespace(x)
11. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
12. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
13. │ │ └─base (local) doWithOneRestart(return(expr), restart)
14. │ └─base::stop(cond)
15. └─purrr (local) `<fn>`(`<pckgNtFE>`)
16. └─cli::cli_abort(...)
17. └─rlang::abort(...)
── Error ('test-drugCodes.R:49:5'): getDrugIngredientCodes working ─────────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1.
i With name: cdm_source.
Caused by error in `loadNamespace()`:
! there is no package called 'arrow'
Backtrace:
▆
1. ├─CodelistGenerator::mockVocabRef(backend = backends[i]) at test-drugCodes.R:49:5
2. │ └─CDMConnector::stow(cdm, dOut)
3. │ └─purrr::walk2(...)
4. │ └─purrr::map2(.x, .y, .f, ..., .progress = .progress)
5. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
6. │ ├─purrr:::with_indexed_errors(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ ├─purrr:::call_with_cleanup(...)
9. │ └─CDMConnector (local) .f(.x[[i]], .y[[i]], ...)
10. ├─base::loadNamespace(x)
11. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
12. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
13. │ │ └─base (local) doWithOneRestart(return(expr), restart)
14. │ └─base::stop(cond)
15. └─purrr (local) `<fn>`(`<pckgNtFE>`)
16. └─cli::cli_abort(...)
17. └─rlang::abort(...)
── Error ('test-drugCodes.R:84:5'): getDrugIngredientCodes expected errors ─────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1.
i With name: cdm_source.
Caused by error in `loadNamespace()`:
! there is no package called 'arrow'
Backtrace:
▆
1. ├─CodelistGenerator::mockVocabRef(backend = backends[i]) at test-drugCodes.R:84:5
2. │ └─CDMConnector::stow(cdm, dOut)
3. │ └─purrr::walk2(...)
4. │ └─purrr::map2(.x, .y, .f, ..., .progress = .progress)
5. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
6. │ ├─purrr:::with_indexed_errors(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ ├─purrr:::call_with_cleanup(...)
9. │ └─CDMConnector (local) .f(.x[[i]], .y[[i]], ...)
10. ├─base::loadNamespace(x)
11. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
12. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
13. │ │ └─base (local) doWithOneRestart(return(expr), restart)
14. │ └─base::stop(cond)
15. └─purrr (local) `<fn>`(`<pckgNtFE>`)
16. └─cli::cli_abort(...)
17. └─rlang::abort(...)
── Error ('test-getCandidateCodes.R:6:5'): tests with mock db ──────────────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1.
i With name: cdm_source.
Caused by error in `loadNamespace()`:
! there is no package called 'arrow'
Backtrace:
▆
1. ├─CodelistGenerator::mockVocabRef(backends[[i]]) at test-getCandidateCodes.R:6:5
2. │ └─CDMConnector::stow(cdm, dOut)
3. │ └─purrr::walk2(...)
4. │ └─purrr::map2(.x, .y, .f, ..., .progress = .progress)
5. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
6. │ ├─purrr:::with_indexed_errors(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ ├─purrr:::call_with_cleanup(...)
9. │ └─CDMConnector (local) .f(.x[[i]], .y[[i]], ...)
10. ├─base::loadNamespace(x)
11. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
12. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
13. │ │ └─base (local) doWithOneRestart(return(expr), restart)
14. │ └─base::stop(cond)
15. └─purrr (local) `<fn>`(`<pckgNtFE>`)
16. └─cli::cli_abort(...)
17. └─rlang::abort(...)
── Error ('test-getICD10StandardCodes.R:4:5'): db without icd10 codes loaded ───
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1.
i With name: cdm_source.
Caused by error in `loadNamespace()`:
! there is no package called 'arrow'
Backtrace:
▆
1. ├─CodelistGenerator::mockVocabRef(backend = backends[i]) at test-getICD10StandardCodes.R:4:5
2. │ └─CDMConnector::stow(cdm, dOut)
3. │ └─purrr::walk2(...)
4. │ └─purrr::map2(.x, .y, .f, ..., .progress = .progress)
5. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
6. │ ├─purrr:::with_indexed_errors(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ ├─purrr:::call_with_cleanup(...)
9. │ └─CDMConnector (local) .f(.x[[i]], .y[[i]], ...)
10. ├─base::loadNamespace(x)
11. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
12. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
13. │ │ └─base (local) doWithOneRestart(return(expr), restart)
14. │ └─base::stop(cond)
15. └─purrr (local) `<fn>`(`<pckgNtFE>`)
16. └─cli::cli_abort(...)
17. └─rlang::abort(...)
── Error ('test-mockVocabRef.R:3:3'): mock vocab db ────────────────────────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1.
i With name: cdm_source.
Caused by error in `loadNamespace()`:
! there is no package called 'arrow'
Backtrace:
▆
1. ├─CodelistGenerator::mockVocabRef("data_frame") at test-mockVocabRef.R:3:3
2. │ └─CDMConnector::stow(cdm, dOut)
3. │ └─purrr::walk2(...)
4. │ └─purrr::map2(.x, .y, .f, ..., .progress = .progress)
5. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
6. │ ├─purrr:::with_indexed_errors(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ ├─purrr:::call_with_cleanup(...)
9. │ └─CDMConnector (local) .f(.x[[i]], .y[[i]], ...)
10. ├─base::loadNamespace(x)
11. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
12. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
13. │ │ └─base (local) doWithOneRestart(return(expr), restart)
14. │ └─base::stop(cond)
15. └─purrr (local) `<fn>`(`<pckgNtFE>`)
16. └─cli::cli_abort(...)
17. └─rlang::abort(...)
── Error ('test-vocabUtilities.R:6:5'): tests with mock db ─────────────────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1.
i With name: cdm_source.
Caused by error in `loadNamespace()`:
! there is no package called 'arrow'
Backtrace:
▆
1. ├─CodelistGenerator::mockVocabRef(backends[[i]]) at test-vocabUtilities.R:6:5
2. │ └─CDMConnector::stow(cdm, dOut)
3. │ └─purrr::walk2(...)
4. │ └─purrr::map2(.x, .y, .f, ..., .progress = .progress)
5. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
6. │ ├─purrr:::with_indexed_errors(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ ├─purrr:::call_with_cleanup(...)
9. │ └─CDMConnector (local) .f(.x[[i]], .y[[i]], ...)
10. ├─base::loadNamespace(x)
11. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
12. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
13. │ │ └─base (local) doWithOneRestart(return(expr), restart)
14. │ └─base::stop(cond)
15. └─purrr (local) `<fn>`(`<pckgNtFE>`)
16. └─cli::cli_abort(...)
17. └─rlang::abort(...)
[ FAIL 9 | WARN 0 | SKIP 5 | PASS 129 ]
Error: Test failures
In addition: There were 14 warnings (use warnings() to see them)
Execution halted
Warning messages:
1: Connection is garbage-collected, use dbDisconnect() to avoid this.
2: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
3: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
4: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
5: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
6: Database is garbage-collected, use dbDisconnect(con, shutdown=TRUE) or duckdb::duckdb_shutdown(drv) to avoid this.
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘a01_Introduction_to_CodelistGenerator.Rmd’ using rmarkdown
Quitting from lines 100-107 [unnamed-chunk-8] (a01_Introduction_to_CodelistGenerator.Rmd)
Error: processing vignette 'a01_Introduction_to_CodelistGenerator.Rmd' failed with diagnostics:
Assigned data `map(.subset(x, unname), vectbl_set_names, NULL)` must be
compatible with existing data.
✖ Existing data has 139 rows.
✖ Element 1 of assigned data has 0 rows.
ℹ Only vectors of size 1 are recycled.
Caused by error in `vectbl_recycle_rhs_rows()`:
! Can't recycle input of size 0 to size 139.
--- failed re-building ‘a01_Introduction_to_CodelistGenerator.Rmd’
--- re-building ‘a02_Candidate_codes_OA.Rmd’ using rmarkdown
--- finished re-building ‘a02_Candidate_codes_OA.Rmd’
--- re-building ‘a03_Options_for_CodelistGenerator.Rmd’ using rmarkdown
--- finished re-building ‘a03_Options_for_CodelistGenerator.Rmd’
--- re-building ‘a04_codelists_for_medications.Rmd’ using rmarkdown
--- finished re-building ‘a04_codelists_for_medications.Rmd’
SUMMARY: processing the following file failed:
‘a01_Introduction_to_CodelistGenerator.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang