Last updated on 2025-05-11 07:50:59 CEST.
| Package | ERROR | OK |
|---|---|---|
| diseasystore | 1 | 12 |
| SCDB | 13 |
Current CRAN status: ERROR: 1, OK: 12
Version: 0.3.1
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [67s/107s]
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$message' failed: Must comply to pattern 'Stratification could not be computed'
[ FAIL 13 | WARN 0 | SKIP 12 | PASS 500 ]
Error: Test failures
In addition: Warning messages:
1: In connection_release(conn@ptr) : Already disconnected
2: call dbDisconnect() when finished working with a connection
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 0.3.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘benchmarks.Rmd’ using rmarkdown
fatal: not a git repository (or any parent up to mount point /Volumes)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
--- finished re-building ‘benchmarks.Rmd’
--- re-building ‘diseasystore-ecdc-respiratory-viruses.Rmd’ using rmarkdown
--- finished re-building ‘diseasystore-ecdc-respiratory-viruses.Rmd’
--- re-building ‘diseasystore-google-covid-19.Rmd’ using rmarkdown
--- finished re-building ‘diseasystore-google-covid-19.Rmd’
--- re-building ‘diseasystore.Rmd’ using rmarkdown
--- finished re-building ‘diseasystore.Rmd’
--- re-building ‘extending-diseasystore-example.Rmd’ using rmarkdown
Warning in file("", "w+b") :
cannot open file '/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T//RtmpdWr5XB/Rf8bba2441fe79': No space left on device
Quitting from extending-diseasystore-example.Rmd:467-469 [ds_available_features]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
Backtrace:
▆
1. └─tools:::.buildOneVignette(...)
2. ├─base::tryCatch(...)
3. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─engine$weave(file, quiet = quiet, encoding = enc)
7. └─knitr:::vweave_rmarkdown(...)
8. └─rmarkdown::render(...)
9. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
10. └─knitr:::process_file(text, output)
11. ├─xfun:::handle_error(...)
12. ├─base::withCallingHandlers(...)
13. └─knitr:::process_group(group)
14. └─knitr:::call_block(x)
15. └─knitr:::block_exec(params)
16. └─knitr:::eng_r(options)
17. ├─knitr:::in_input_dir(...)
18. │ └─knitr:::in_dir(input_dir(), expr)
19. └─knitr (local) evaluate(...)
20. └─evaluate::evaluate(...)
21. └─evaluate:::watchout(...)
22. └─evaluate:::local_persistent_sink_connection(debug, frame)
23. └─base::file("", "w+b")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'extending-diseasystore-example.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘extending-diseasystore-example.Rmd’
Warning: Connection already closed.
SUMMARY: processing the following file failed:
‘extending-diseasystore-example.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64
Current CRAN status: OK: 13