CRAN Package Check Results for Package PhenotypeR

Last updated on 2025-08-03 01:49:44 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.6 4.75 413.69 418.44 OK
r-devel-linux-x86_64-debian-gcc 0.2.0 3.66 425.48 429.14 OK
r-devel-linux-x86_64-fedora-clang 0.2.0 842.47 OK
r-devel-linux-x86_64-fedora-gcc 0.2.0 881.39 OK
r-devel-windows-x86_64 0.1.6 7.00 229.00 236.00 OK
r-patched-linux-x86_64 0.1.6 4.56 389.11 393.67 OK
r-release-linux-x86_64 0.2.0 4.94 531.15 536.09 OK
r-release-macos-arm64 0.2.0 357.00 OK
r-release-macos-x86_64 0.2.0 251.00 ERROR
r-release-windows-x86_64 0.2.0 9.00 385.00 394.00 OK
r-oldrel-macos-arm64 0.2.0 367.00 NOTE
r-oldrel-macos-x86_64 0.2.0 317.00 ERROR
r-oldrel-windows-x86_64 0.2.0 9.00 480.00 489.00 NOTE

Check Details

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://example-data.ohdsi.dev/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB Quitting from CodelistDiagnostics.Rmd:28-56 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': rapi_startup: Failed to open database: {"exception_type":"IO","exception_message":"Could not write file \"/private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/Rtmpow2WbY/synpuf-1k_5.3_1.3.duckdb\": No space left on device","errno":"28"} --- Backtrace: ▆ 1. ├─DBI::dbConnect(...) 2. ├─DBI::dbConnect(...) 3. │ └─duckdb (local) .local(drv, ...) 4. │ └─duckdb:::path_normalize(dbdir) 5. ├─CDMConnector::eunomiaDir("synpuf-1k", "5.3") 6. │ ├─DBI::dbConnect(duckdb::duckdb(datasetLocation)) 7. │ └─duckdb::duckdb(datasetLocation) 8. │ ├─methods::new(...) 9. │ │ ├─methods::initialize(value, ...) 10. │ │ └─methods::initialize(value, ...) 11. │ └─duckdb:::rethrow_rapi_startup(dbdir, read_only, config, environment_scan) 12. │ ├─rlang::try_fetch(...) 13. │ │ ├─base::tryCatch(...) 14. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 15. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 16. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 17. │ │ └─base::withCallingHandlers(...) 18. │ └─duckdb:::rapi_startup(dbdir, readonly, configsexp, environment_scan) 19. ├─base::.handleSimpleError(...) 20. │ └─rlang (local) h(simpleError(msg, call)) 21. │ └─handlers[[1L]](cnd) 22. │ └─duckdb:::rethrow_error_from_rapi(e, call) 23. │ └─rlang::abort(msg, call = call) 24. │ └─rlang:::signal_abort(cnd, .file) 25. │ └─base::signalCondition(cnd) 26. └─base (local) `<fn>`(`<rlng_rrr>`) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'CodelistDiagnostics.Rmd' failed with diagnostics: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': rapi_startup: Failed to open database: {"exception_type":"IO","exception_message":"Could not write file \"/private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/Rtmpow2WbY/synpuf-1k_5.3_1.3.duckdb\": No space left on device","errno":"28"} --- 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://example-data.ohdsi.dev/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB Quitting from DatabaseDiagnostics.Rmd:26-40 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': rapi_startup: Failed to open database: {"exception_type":"IO","exception_message":"Could not write file \"/private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/RtmpIC3JPE/synpuf-1k_5.3_1.3.duckdb\": No space left on device","errno":"28"} --- Backtrace: ▆ 1. ├─DBI::dbConnect(...) 2. ├─DBI::dbConnect(...) 3. │ └─duckdb (local) .local(drv, ...) 4. │ └─duckdb:::path_normalize(dbdir) 5. ├─CDMConnector::eunomiaDir("synpuf-1k", "5.3") 6. │ ├─DBI::dbConnect(duckdb::duckdb(datasetLocation)) 7. │ └─duckdb::duckdb(datasetLocation) 8. │ ├─methods::new(...) 9. │ │ ├─methods::initialize(value, ...) 10. │ │ └─methods::initialize(value, ...) 11. │ └─duckdb:::rethrow_rapi_startup(dbdir, read_only, config, environment_scan) 12. │ ├─rlang::try_fetch(...) 13. │ │ ├─base::tryCatch(...) 14. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 15. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 16. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 17. │ │ └─base::withCallingHandlers(...) 18. │ └─duckdb:::rapi_startup(dbdir, readonly, configsexp, environment_scan) 19. ├─base::.handleSimpleError(...) 20. │ └─rlang (local) h(simpleError(msg, call)) 21. │ └─handlers[[1L]](cnd) 22. │ └─duckdb:::rethrow_error_from_rapi(e, call) 23. │ └─rlang::abort(msg, call = call) 24. │ └─rlang:::signal_abort(cnd, .file) 25. │ └─base::signalCondition(cnd) 26. └─base (local) `<fn>`(`<rlng_rrr>`) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'DatabaseDiagnostics.Rmd' failed with diagnostics: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': rapi_startup: Failed to open database: {"exception_type":"IO","exception_message":"Could not write file \"/private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/RtmpIC3JPE/synpuf-1k_5.3_1.3.duckdb\": No space left on device","errno":"28"} --- failed re-building ‘DatabaseDiagnostics.Rmd’ --- re-building ‘PhenotypeDiagnostics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/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://example-data.ohdsi.dev/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB Quitting from PopulationDiagnostics.Rmd:26-48 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error: ! error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': rapi_startup: Failed to open database: {"exception_type":"IO","exception_message":"Could not write file \"/private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/Rtmptt8j5w/synpuf-1k_5.3_1.3.duckdb\": No space left on device","errno":"28"} --- Backtrace: ▆ 1. ├─DBI::dbConnect(...) 2. ├─DBI::dbConnect(...) 3. │ └─duckdb (local) .local(drv, ...) 4. │ └─duckdb:::path_normalize(dbdir) 5. ├─CDMConnector::eunomiaDir("synpuf-1k", "5.3") 6. │ ├─DBI::dbConnect(duckdb::duckdb(datasetLocation)) 7. │ └─duckdb::duckdb(datasetLocation) 8. │ ├─methods::new(...) 9. │ │ ├─methods::initialize(value, ...) 10. │ │ └─methods::initialize(value, ...) 11. │ └─duckdb:::rethrow_rapi_startup(dbdir, read_only, config, environment_scan) 12. │ ├─rlang::try_fetch(...) 13. │ │ ├─base::tryCatch(...) 14. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 15. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 16. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 17. │ │ └─base::withCallingHandlers(...) 18. │ └─duckdb:::rapi_startup(dbdir, readonly, configsexp, environment_scan) 19. ├─base::.handleSimpleError(...) 20. │ └─rlang (local) h(simpleError(msg, call)) 21. │ └─handlers[[1L]](cnd) 22. │ └─duckdb:::rethrow_error_from_rapi(e, call) 23. │ └─rlang::abort(msg, call = call) 24. │ └─rlang:::signal_abort(cnd, .file) 25. │ └─base::signalCondition(cnd) 26. └─base (local) `<fn>`(`<rlng_rrr>`) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'PopulationDiagnostics.Rmd' failed with diagnostics: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': rapi_startup: Failed to open database: {"exception_type":"IO","exception_message":"Could not write file \"/private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/Rtmptt8j5w/synpuf-1k_5.3_1.3.duckdb\": No space left on device","errno":"28"} --- failed re-building ‘PopulationDiagnostics.Rmd’ --- re-building ‘ShinyDiagnostics.Rmd’ using rmarkdown --- finished re-building ‘ShinyDiagnostics.Rmd’ SUMMARY: processing the following files failed: ‘CodelistDiagnostics.Rmd’ ‘DatabaseDiagnostics.Rmd’ ‘PopulationDiagnostics.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-release-macos-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: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘CodelistDiagnostics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB Quitting from CodelistDiagnostics.Rmd:28-56 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'CodelistDiagnostics.Rmd' failed with diagnostics: File copy from /var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T//RtmpnG3Eog/synpuf-1k_5.3_1.3.duckdb to /var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T//RtmpnG3Eog/file2a1a79826cdb.duckdb failed! --- 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://example-data.ohdsi.dev/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB Quitting from DatabaseDiagnostics.Rmd:26-40 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'DatabaseDiagnostics.Rmd' failed with diagnostics: File copy from /var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T//RtmprHdHus/synpuf-1k_5.3_1.3.duckdb to /var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T//RtmprHdHus/file2fdf398952b0.duckdb failed! --- failed re-building ‘DatabaseDiagnostics.Rmd’ --- re-building ‘PhenotypeDiagnostics.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/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://example-data.ohdsi.dev/synpuf-1k_5.3.zip' Content type 'application/zip' length 593048982 bytes (565.6 MB) ================================================== downloaded 565.6 MB Quitting from PopulationDiagnostics.Rmd:26-48 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'PopulationDiagnostics.Rmd' failed with diagnostics: File copy from /var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T//Rtmpy3Jg7q/synpuf-1k_5.3_1.3.duckdb to /var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T//Rtmpy3Jg7q/file317854df31ea.duckdb failed! --- failed re-building ‘PopulationDiagnostics.Rmd’ --- re-building ‘ShinyDiagnostics.Rmd’ using rmarkdown --- finished re-building ‘ShinyDiagnostics.Rmd’ SUMMARY: processing the following files failed: ‘CodelistDiagnostics.Rmd’ ‘DatabaseDiagnostics.Rmd’ ‘PopulationDiagnostics.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-oldrel-macos-x86_64