Check results for 'diseasystore'

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
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘diseasystore’ can be installed ... [10s/13s] 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 code 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
checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
checking loading without being on the library search path ... [1s/1s] OK
checking whether startup messages can be suppressed ... [1s/1s] OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [4s/5s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking contents of ‘data’ directory ... OK
checking data for non-ASCII characters ... [0s/0s] OK
checking LazyData ... OK
checking data for ASCII and uncompressed saves ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [2s/2s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [65s/97s] ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [64s/97s] 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 ... [56s/61s] 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 '