Last updated on 2025-10-21 00:50:50 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| diseasystore | 2 | 1 | 10 |
| SCDB | 1 | 12 |
Current CRAN status: ERROR: 2, NOTE: 1, OK: 10
Version: 0.3.2
Check: HTML version of manual
Result: NOTE
Found the following HTML validation problems:
DiseasystoreBase.html:169:1 (DiseasystoreBase.Rd:119): Warning: <h5> anchor "Usage" already defined
DiseasystoreBase.html:180:1 (DiseasystoreBase.Rd:128): Warning: <h5> anchor "Arguments" already defined
DiseasystoreBase.html:200:1 (DiseasystoreBase.Rd:142): Warning: <h5> anchor "Returns" already defined
DiseasystoreBase.html:218:1 (DiseasystoreBase.Rd:152): Warning: <h5> anchor "Usage" already defined
DiseasystoreBase.html:229:1 (DiseasystoreBase.Rd:161): Warning: <h5> anchor "Arguments" already defined
DiseasystoreBase.html:248:1 (DiseasystoreBase.Rd:174): Warning: <h5> anchor "Returns" already defined
DiseasystoreBase.html:265:1 (DiseasystoreBase.Rd:183): Warning: <h5> anchor "Usage" already defined
DiseasystoreBase.html:271:1 (DiseasystoreBase.Rd:187): Warning: <h5> anchor "Arguments" already defined
DiseasystoreEcdcRespiratoryViruses.html:112:1 (DiseasystoreEcdcRespiratoryViruses.Rd:68): Warning: <h5> anchor "Usage" already defined
DiseasystoreEcdcRespiratoryViruses.html:118:1 (DiseasystoreEcdcRespiratoryViruses.Rd:72): Warning: <h5> anchor "Arguments" already defined
DiseasystoreSimulist.html:110:1 (DiseasystoreSimulist.Rd:66): Warning: <h5> anchor "Usage" already defined
DiseasystoreSimulist.html:116:1 (DiseasystoreSimulist.Rd:70): Warning: <h5> anchor "Arguments" already defined
FeatureHandler.html:149:1 (FeatureHandler.Rd:126): Warning: <h5> anchor "Usage" already defined
FeatureHandler.html:155:1 (FeatureHandler.Rd:130): Warning: <h5> anchor "Arguments" already defined
Flavor: r-devel-linux-x86_64-debian-gcc
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
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 0.3.2
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [63s/98s]
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.
#####
Following backends will be tested:
####
This message is displayed once per session.
[ FAIL 13 | WARN 0 | SKIP 12 | PASS 500 ]
══ 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$get_feature(feature)` to run without any errors.
i Actually got a <purrr_error_indexed> with text:
i In index: 1.
Caused by error:
! vector memory limit of 16.0 Gb reached, see mem.maxVSize()
── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can initialise with default source_conn ──
Expected `ds$get_feature(ds$available_features[[1]])` to run without any errors.
i Actually got a <purrr_error_indexed> with text:
i In index: 1.
Caused by error:
! vector memory limit of 16.0 Gb reached, see mem.maxVSize()
── Error ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can retrieve features from a fresh state ──
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1.
Caused by error in `pmap()`:
i In index: 1.
Caused by error:
! vector memory limit of 16.0 Gb reached, see mem.maxVSize()
── Error ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can extend existing features ──
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1.
Caused by error in `pmap()`:
i In index: 1.
Caused by error:
! vector memory limit of 16.0 Gb reached, see mem.maxVSize()
── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ──
Expected `ds$key_join_features(...)` to run without any errors.
i Actually got a <purrr_error_indexed> with text:
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$key_join_features(...)` to run without any errors.
i Actually got a <purrr_error_indexed> with text:
i In index: 1.
Caused by error:
! vector memory limit of 16.0 Gb reached, see mem.maxVSize()
── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ──
Expected `ds$key_join_features(...)` to run without any errors.
i Actually got a <purrr_error_indexed> with text:
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$key_join_features(...)` to run without any errors.
i Actually got a <purrr_error_indexed> with text:
i In index: 1.
Caused by error:
! vector memory limit of 16.0 Gb reached, see mem.maxVSize()
── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ──
Expected `ds$key_join_features(...)` to run without any errors.
i Actually got a <purrr_error_indexed> with text:
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$key_join_features(...)` to run without any errors.
i Actually got a <purrr_error_indexed> with text:
i In index: 1.
Caused by error:
! vector memory limit of 16.0 Gb reached, see mem.maxVSize()
── Error ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ──
<purrr_error_indexed/rlang_error/error/condition>
Error in `pmap(.l, .f, ..., .progress = .progress)`: i In index: 1.
Caused by error:
! e$message (`actual`) not identical to paste("(At least one) stratification feature does not match observable aggregator. Not implemented yet.") (`expected`).
`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'
[ FAIL 13 | WARN 0 | SKIP 12 | PASS 500 ]
Error: Test failures
In addition: 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
Current CRAN status: NOTE: 1, OK: 12
Version: 0.5.1
Check: HTML version of manual
Result: NOTE
Found the following HTML validation problems:
Logger.html:171:1 (Logger.Rd:120): Warning: <h5> anchor "Usage" already defined
Logger.html:183:1 (Logger.Rd:130): Warning: <h5> anchor "Arguments" already defined
Logger.html:226:1 (Logger.Rd:159): Warning: <h5> anchor "Usage" already defined
Logger.html:232:1 (Logger.Rd:163): Warning: <h5> anchor "Arguments" already defined
Logger.html:259:1 (Logger.Rd:180): Warning: <h5> anchor "Usage" already defined
Logger.html:265:1 (Logger.Rd:184): Warning: <h5> anchor "Arguments" already defined
Logger.html:292:1 (Logger.Rd:201): Warning: <h5> anchor "Usage" already defined
Logger.html:298:1 (Logger.Rd:205): Warning: <h5> anchor "Arguments" already defined
Logger.html:323:1 (Logger.Rd:220): Warning: <h5> anchor "Usage" already defined
Logger.html:329:1 (Logger.Rd:224): Warning: <h5> anchor "Arguments" already defined
Logger.html:353:1 (Logger.Rd:238): Warning: <h5> anchor "Usage" already defined
Logger.html:359:1 (Logger.Rd:242): Warning: <h5> anchor "Arguments" already defined
LoggerNull.html:111:1 (LoggerNull.Rd:64): Warning: <h5> anchor "Usage" already defined
LoggerNull.html:117:1 (LoggerNull.Rd:68): Warning: <h5> anchor "Arguments" already defined
LoggerNull.html:140:1 (LoggerNull.Rd:81): Warning: <h5> anchor "Usage" already defined
LoggerNull.html:146:1 (LoggerNull.Rd:85): Warning: <h5> anchor "Arguments" already defined
LoggerNull.html:169:1 (LoggerNull.Rd:98): Warning: <h5> anchor "Usage" already defined
LoggerNull.html:175:1 (LoggerNull.Rd:102): Warning: <h5> anchor "Arguments" already defined
Flavor: r-devel-linux-x86_64-debian-gcc