CRAN Package Check Results for Package diseasystore

Last updated on 2025-11-19 07:49:43 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.3.2	16.52	518.11	534.63	OK
r-devel-linux-x86_64-debian-gcc	0.3.2	10.99	378.62	389.61	OK
r-devel-linux-x86_64-fedora-clang	0.3.2	65.00	807.93	872.93	OK
r-devel-linux-x86_64-fedora-gcc	0.3.2	52.00	759.54	811.54	OK
r-devel-windows-x86_64	0.3.2	22.00	471.00	493.00	OK
r-patched-linux-x86_64	0.3.2	13.50	504.86	518.36	OK
r-release-linux-x86_64	0.3.2	15.21	496.40	511.61	OK
r-release-macos-arm64	0.3.2	5.00	211.00	216.00	OK
r-release-macos-x86_64	0.3.2	27.00	766.00	793.00	OK
r-release-windows-x86_64	0.3.2	18.00	467.00	485.00	OK
r-oldrel-macos-arm64	0.3.2	5.00	206.00	211.00	OK
r-oldrel-macos-x86_64	0.3.2	16.00	189.00	205.00	ERROR
r-oldrel-windows-x86_64	0.3.2	23.00	642.00	665.00	OK

Check Details

Version: 0.3.2
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [62s/72s] 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) > > test_check("diseasystore") Loading required package: diseasystore ##### Following backends will be tested: SQLite #### This message is displayed once per session. Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R ##### Following backends will be tested: #### This message is displayed once per session. Saving _problems/test-zzz-12.R [ FAIL 14 | WARN 0 | SKIP 12 | PASS 499 ] ══ Skipped tests (12) ══════════════════════════════════════════════════════════ • "SQLiteConnection" %in% skip_backends is TRUE (3): 'test-DiseasystoreSimulist.R:2:1', 'test-DiseasystoreSimulist.R:2:1', 'test-DiseasystoreSimulist.R:2:1' • Skip if running in R_check (1): 'test-0_linters.R:64:3' • empty test (5): 'test-DiseasystoreSimulist.R:2:1', 'test-DiseasystoreSimulist.R:2:1', 'test-DiseasystoreSimulist.R:2:1', 'test-DiseasystoreSimulist.R:2:1', 'test-DiseasystoreSimulist.R:2:1' • is.null(skip_backends) is TRUE (2): 'test-DiseasystoreEcdcRespitoryViruses.R:7:1', 'test-DiseasystoreGoogleCovid19.R:5:1' • remote_data_available is not TRUE (1): 'test-DiseasystoreEcdcRespitoryViruses.R:7:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can initialise with remote source_conn ── Expected `ds$get_feature(feature)` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error: ! vector memory limit of 16.0 Gb reached, see mem.maxVSize() ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can initialise with default source_conn ── Expected `ds$get_feature(ds$available_features[[1]])` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error: ! vector memory limit of 16.0 Gb reached, see mem.maxVSize() ── Error ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can retrieve features from a fresh state ── <purrr_error_indexed/rlang_error/error/condition> Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1. Caused by error in `pmap()`: i In index: 1. Caused by error: ! vector memory limit of 16.0 Gb reached, see mem.maxVSize() ── Error ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can extend existing features ── <purrr_error_indexed/rlang_error/error/condition> Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1. Caused by error in `pmap()`: i In index: 1. Caused by error: ! vector memory limit of 16.0 Gb reached, see mem.maxVSize() ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error: ! vector memory limit of 16.0 Gb reached, see mem.maxVSize() ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error: ! vector memory limit of 16.0 Gb reached, see mem.maxVSize() ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error: ! vector memory limit of 16.0 Gb reached, see mem.maxVSize() ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error: ! vector memory limit of 16.0 Gb reached, see mem.maxVSize() ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error: ! vector memory limit of 16.0 Gb reached, see mem.maxVSize() ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error: ! vector memory limit of 16.0 Gb reached, see mem.maxVSize() ── Error ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── <purrr_error_indexed/rlang_error/error/condition> Error in `pmap(.l, .f, ..., .progress = .progress)`: i In index: 1. Caused by error: ! Expected `e$message` to be identical to `paste("(At least one) stratification feature does not match observable aggregator. Not implemented yet.")`. Differences: `names(actual)` is a character vector ('i') `names(expected)` is absent actual vs expected - i"In index: 1." + "(At least one) stratification feature does not match observable aggregator. Not implemented yet." ── Error ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join with feature-independent stratification ── <purrr_error_indexed/rlang_error/error/condition> Error in `pmap(.l, .f, ..., .progress = .progress)`: i In index: 1. Caused by error: ! vector memory limit of 16.0 Gb reached, see mem.maxVSize() Backtrace: ▆ 1. ├─ds$key_join_features(...) 2. │ └─self$get_feature(observable, start_date, end_date) 3. │ └─purrr::pwalk(...) 4. │ └─purrr::pmap(.l, .f, ..., .progress = .progress) 5. │ └─purrr:::pmap_("list", .l, .f, ..., .progress = .progress) 6. │ ├─purrr:::with_indexed_errors(...) 7. │ │ └─base::withCallingHandlers(...) 8. │ ├─purrr:::call_with_cleanup(...) 9. │ └─diseasystore (local) .f(start_date = .l[[1L]][[i]], end_date = .l[[2L]][[i]], ...) 10. │ ├─base::do.call(...) 11. │ └─diseasystore (local) `<fn>`(...) 12. │ ├─dplyr::mutate(...) 13. │ ├─dplyr::select(...) 14. │ ├─tidyr::unite(...) 15. │ ├─dplyr::mutate(...) 16. │ ├─tidyr::pivot_longer(...) 17. │ └─tidyr:::pivot_longer.data.frame(...) 18. │ └─tidyr::build_longer_spec(...) 19. │ └─tidyr:::str_separate(names, names_to, sep = names_sep, error_call = error_call) 20. │ └─tidyr:::str_split_fixed(...) 21. │ └─tidyr:::simplifyPieces(pieces, n, fill == "left") 22. └─base::.handleSimpleError(...) 23. └─purrr (local) h(simpleError(msg, call)) 24. └─cli::cli_abort(...) 25. └─rlang::abort(...) ── Error ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 key_join fails gracefully ── <purrr_error_indexed/rlang_error/error/condition> Error in `pmap(.l, .f, ..., .progress = .progress)`: i In index: 1. Caused by error: ! Check on 'e$message' failed: Must comply to pattern 'Stratification could not be computed' ── Failure ('test-zzz.R:12:3'): data is not written locally ──────────────────── Expected `dir(recursive = TRUE)` to have the same values as `current_files`. Actual: "_problems/test-DiseasystoreGoogleCovid19-11.R", "helper-setup.R", "setup.R", "test-0_R6_utils.R", "test-0_documentation.R", "test-0_linters.R", "test-0_rd_files.R", "test-DiseasystoreBase.R", "test-DiseasystoreEcdcRespitoryViruses.R", ... Expected: "helper-setup.R", "setup.R", "test-0_R6_utils.R", "test-0_documentation.R", "test-0_linters.R", "test-0_rd_files.R", "test-DiseasystoreBase.R", "test-DiseasystoreEcdcRespitoryViruses.R", "test-DiseasystoreGoogleCovid19.R", ... Needs: "_problems/test-DiseasystoreGoogleCovid19-11.R" [ FAIL 14 | WARN 0 | SKIP 12 | PASS 499 ] Error: ! Test failures. Warning messages: 1: In connection_release(conn@ptr) : Already disconnected 2: call dbDisconnect() when finished working with a connection Execution halted Flavor: r-oldrel-macos-x86_64

Version: 0.3.2
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘benchmarks.Rmd’ using rmarkdown fatal: not a git repository (or any parent up to mount point /Volumes) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). --- finished re-building ‘benchmarks.Rmd’ --- re-building ‘diseasystore-ecdc-respiratory-viruses.Rmd’ using rmarkdown --- finished re-building ‘diseasystore-ecdc-respiratory-viruses.Rmd’ --- re-building ‘diseasystore-google-covid-19.Rmd’ using rmarkdown --- finished re-building ‘diseasystore-google-covid-19.Rmd’ --- re-building ‘diseasystore.Rmd’ using rmarkdown --- finished re-building ‘diseasystore.Rmd’ --- re-building ‘extending-diseasystore-example.Rmd’ using rmarkdown Quitting from extending-diseasystore-example.Rmd:536-540 [stratifications_positive_sex_age_plot] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'extending-diseasystore-example.Rmd' failed with diagnostics: Faceting variables must have at least one value. --- failed re-building ‘extending-diseasystore-example.Rmd’ Warning: Connection already closed. --- re-building ‘extending-diseasystore.Rmd’ using rmarkdown --- finished re-building ‘extending-diseasystore.Rmd’ SUMMARY: processing the following file failed: ‘extending-diseasystore-example.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-oldrel-macos-x86_64