Check results for 'diseasystore'

using R version 4.4.3 Patched (2026-02-12 r89409)
using platform: aarch64-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 13.7.8
using session charset: UTF-8
checking for file ‘diseasystore/DESCRIPTION’ ... OK
this is package ‘diseasystore’ version ‘0.3.3’
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 ... [3s/3s] 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 ... [0s/0s] OK
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checking loading without being on the library search path ... [0s/0s] OK
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checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
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checking R code for possible problems ... [1s/1s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
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checking for unstated dependencies in examples ... OK
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 ... [1s/1s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [32s/37s] ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [31s/37s] 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. Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R Saving _problems/test-DiseasystoreGoogleCovid19-11.R ##### Following backends will be tested: #### This message is displayed once per session. Saving _problems/test-zzz-12.R [ FAIL 14 | WARN 0 | SKIP 12 | PASS 530 ] ══ 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$get_feature(feature)` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error in `simplifyPieces()`: ! SET_VECTOR_ELT() can only be applied to a 'list', not a 'promise' ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can initialise with default source_conn ── Expected `ds$get_feature(ds$available_features[[1]])` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error in `simplifyPieces()`: ! SET_VECTOR_ELT() can only be applied to a 'list', not a 'promise' ── Error ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can retrieve features from a fresh state ── <purrr_error_indexed/rlang_error/error/condition> Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1. Caused by error in `pmap()`: i In index: 1. Caused by error in `simplifyPieces()`: ! SET_VECTOR_ELT() can only be applied to a 'list', not a 'promise' ── Error ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can extend existing features ── <purrr_error_indexed/rlang_error/error/condition> Error in `map2(.x, .y, .f, ..., .progress = .progress)`: i In index: 1. Caused by error in `pmap()`: i In index: 1. Caused by error in `simplifyPieces()`: ! SET_VECTOR_ELT() can only be applied to a 'list', not a 'promise' ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error in `simplifyPieces()`: ! SET_VECTOR_ELT() can only be applied to a 'list', not a 'promise' ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error in `simplifyPieces()`: ! SET_VECTOR_ELT() can only be applied to a 'list', not a 'promise' ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error in `simplifyPieces()`: ! SET_VECTOR_ELT() can only be applied to a 'list', not a 'promise' ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error in `simplifyPieces()`: ! SET_VECTOR_ELT() can only be applied to a 'list', not a 'promise' ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error in `simplifyPieces()`: ! SET_VECTOR_ELT() can only be applied to a 'list', not a 'promise' ── Failure ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── Expected `ds$key_join_features(...)` not to throw any errors. Actually got a <purrr_error_indexed> with message: i In index: 1. Caused by error in `simplifyPieces()`: ! SET_VECTOR_ELT() can only be applied to a 'list', not a 'promise' ── Error ('test-DiseasystoreGoogleCovid19.R:5:1'): DiseasystoreGoogleCovid19 can key_join features ── <purrr_error_indexed/rlang_error/error/condition> Error in `pmap(.l, .f, ..., .progress = .progress)`: i In index: 1. Caused by error: ! Expected `e$message` to be identical to `paste("(At least one) stratification feature does not match observable aggregator. Not implemented yet.")`. Differences: `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 in `simplifyPieces()`: ! SET_VECTOR_ELT() can only be applied to a 'list', not a 'promise' 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' ── Failure ('test-zzz.R:12:3'): data is not written locally ──────────────────── Expected `dir(recursive = TRUE)` to have the same values as `current_files`. Actual: "_problems/test-DiseasystoreGoogleCovid19-11.R", "helper-setup.R", "setup.R", "test-0_R6_utils.R", "test-0_documentation.R", "test-0_linters.R", "test-0_rd_files.R", "test-DiseasystoreBase.R", "test-DiseasystoreEcdcRespitoryViruses.R", ... Expected: "helper-setup.R", "setup.R", "test-0_R6_utils.R", "test-0_documentation.R", "test-0_linters.R", "test-0_rd_files.R", "test-DiseasystoreBase.R", "test-DiseasystoreEcdcRespitoryViruses.R", "test-DiseasystoreGoogleCovid19.R", ... Needs: "_problems/test-DiseasystoreGoogleCovid19-11.R" [ FAIL 14 | WARN 0 | SKIP 12 | PASS 530 ] Error: ! Test failures. 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 ... [23s/22s] OK
checking PDF version of manual ... [2s/2s] OK
DONE Status: 1 ERROR
using check arguments '--no-clean-on-error '