• using R version 4.4.1 (2024-06-14)
  • using platform: x86_64-apple-darwin20
  • R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 12.2.0
  • running under: macOS Ventura 13.3.1
  • using session charset: UTF-8
  • checking for file ‘diseasystore/DESCRIPTION’ ... OK
  • this is package ‘diseasystore’ version ‘0.3.1’
  • package encoding: UTF-8
  • checking package namespace information ... OK
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  • checking whether package ‘diseasystore’ can be installed ... [10s/16s] OK See the install log for details.
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  • checking package directory ... OK
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  • checking DESCRIPTION meta-information ... OK
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  • checking dependencies in R code ... OK
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  • checking examples ... [2s/3s] OK
  • checking for unstated dependencies in ‘tests’ ... OK
  • checking tests ... [54s/59s] ERROR   Running ‘spelling.R’ [0s/0s]   Running ‘testthat.R’ [53s/58s] 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
  • checking for unstated dependencies in vignettes ... OK
  • checking package vignettes ... OK
  • checking re-building of vignette outputs ... [44s/44s] 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
  • checking PDF version of manual ... [5s/5s] OK
  • DONE Status: 2 ERRORs
  • using check arguments '--no-clean-on-error '