Check results for 'diseasystore'

using R version 4.3.3 (2024-02-29)
using platform: x86_64-apple-darwin20 (64-bit)
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
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
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checking whether package ‘diseasystore’ can be installed ... [9s/11s] OK See the install log for details.
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking R files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... [1s/1s] OK
checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
checking whether the package can be unloaded cleanly ... [1s/1s] OK
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checking loading without being on the library search path ... [1s/1s] OK
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checking dependencies in R code ... OK
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checking R code for possible problems ... [4s/4s] OK
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checking contents of ‘data’ directory ... OK
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checking data for ASCII and uncompressed saves ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [2s/3s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [63s/84s] ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [62s/83s] 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$get_feature(feature)` to run without any errors. i Actually got a <purrr_error_indexed> with text: i In index: 1. Caused by error: ! vector memory exhausted (limit reached?) ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can initialise with default source_conn ── Expected `ds$get_feature(ds$available_features[[1]])` to run without any errors. i Actually got a <purrr_error_indexed> with text: i In index: 1. Caused by error: ! vector memory exhausted (limit reached?) ── Error ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can retrieve features from a fresh state ── <purrr_error_indexed/rlang_error/error/condition> Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1. Caused by error in `pmap()`: i In index: 1. Caused by error: ! vector memory exhausted (limit reached?) ── Error ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can extend existing features ── <purrr_error_indexed/rlang_error/error/condition> Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1. Caused by error in `pmap()`: i In index: 1. Caused by error: ! vector memory exhausted (limit reached?) ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$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 exhausted (limit reached?) ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` to run without any errors. i Actually got a <purrr_error_indexed> with text: i In index: 1. Caused by error: ! vector memory exhausted (limit reached?) ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$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 exhausted (limit reached?) ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` to run without any errors. i Actually got a <purrr_error_indexed> with text: i In index: 1. Caused by error: ! vector memory exhausted (limit reached?) ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$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 exhausted (limit reached?) ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` to run without any errors. i Actually got a <purrr_error_indexed> with text: i In index: 1. Caused by error: ! vector memory exhausted (limit reached?) ── Error ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── <purrr_error_indexed/rlang_error/error/condition> Error in `pmap(.l, .f, ..., .progress = .progress)`: i In index: 1. Caused by error: ! e$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 exhausted (limit reached?) 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 in ‘inst/doc’ ... OK
checking re-building of vignette outputs ... [59s/75s] 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 lines 537-540 [stratifications_positive_sex_age_plot] (extending-diseasystore-example.Rmd) 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 ... [6s/7s] OK
DONE Status: 2 ERRORs
using check arguments '--no-clean-on-error '