Package check result: NOTE Check: CRAN incoming feasibility, Result: NOTE Maintainer: ‘Hadley Wickham ’ New maintainer: Hadley Wickham Old maintainer(s): Hadley Wickham Changes to worse in reverse depends: Package: annotater Check: tests New result: ERROR Running ‘testthat.R’ [4s/4s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(annotater) > > test_check("annotater") [ FAIL 2 | WARN 0 | SKIP 0 | PASS 35 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-overall-annotation.R:78:3'): if statement for pacman calls works ── Error in `stringi::stri_replace_all_fixed(str = string_og, pattern = pck_descs$call, replacement = pck_descs$annotated, vectorize_all = FALSE)`: vector length not consistent with other arguments Backtrace: ▆ 1. ├─testthat::expect_match(annotate_repostitle(test_string), "# Functional") at test-overall-annotation.R:78:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─annotater::annotate_repostitle(test_string) 5. └─stringi::stri_replace_all_fixed(...) ── Failure ('test-overall-annotation.R:86:3'): if statement for pacman + base calls works ── annotate_repostitle\(test_string\) does not match "# Functional". Actual value: "p_load\(purrr\)\\nlibrary\(tidyr\) # Tidy Messy Data CRAN v1\.3\.1" Backtrace: ▆ 1. └─testthat::expect_match(annotate_repostitle(test_string), "# Functional") at test-overall-annotation.R:86:3 2. └─testthat:::expect_match_(...) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 35 ] Error: Test failures Execution halted Package: cfr Check: examples New result: ERROR Running examples in ‘cfr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cfr_rolling > ### Title: Estimate static severity for an expanding time series > ### Aliases: cfr_rolling > > ### ** Examples > > # load package data > data("ebola1976") > > # estimate severity without correcting for delays > cfr_static(ebola1976) Error in cfr_static(ebola1976) : Input data must have sequential dates with none missing or duplicated Calls: cfr_static -> stopifnot Execution halted Package: cfr Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘cfr.Rmd’ using rmarkdown Quitting from lines 93-97 [unnamed-chunk-3] (cfr.Rmd) Error: processing vignette 'cfr.Rmd' failed with diagnostics: Input data must have sequential dates with none missing or duplicated --- failed re-building ‘cfr.Rmd’ --- re-building ‘data_from_incidence2.Rmd’ using rmarkdown --- finished re-building ‘data_from_incidence2.Rmd’ --- re-building ‘delay_distributions.Rmd’ using rmarkdown Quitting from lines 90-98 [unnamed-chunk-4] (delay_distributions.Rmd) Error: processing vignette 'delay_distributions.Rmd' failed with diagnostics: Input data must have sequential dates with none missing or duplicated --- failed re-building ‘delay_distributions.Rmd’ --- re-building ‘estimate_ascertainment.Rmd’ using rmarkdown Quitting from lines 115-121 [unnamed-chunk-3] (estimate_ascertainment.Rmd) Error: processing vignette 'estimate_ascertainment.Rmd' failed with diagnostics: Input data must have sequential dates with none missing or duplicated --- failed re-building ‘estimate_ascertainment.Rmd’ --- re-building ‘estimate_static_severity.Rmd’ using rmarkdown Quitting from lines 120-130 [unnamed-chunk-4] (estimate_static_severity.Rmd) Error: processing vignette 'estimate_static_severity.Rmd' failed with diagnostics: Input data must have sequential dates with none missing or duplicated --- failed re-building ‘estimate_static_severity.Rmd’ --- re-building ‘estimate_time_varying_severity.Rmd’ using rmarkdown Quitting from lines 113-133 [unnamed-chunk-4] (estimate_time_varying_severity.Rmd) Error: processing vignette 'estimate_time_varying_severity.Rmd' failed with diagnostics: Input data must have sequential dates with none missing or duplicated --- failed re-building ‘estimate_time_varying_severity.Rmd’ --- re-building ‘software-permissions.Rmd’ using rmarkdown --- finished re-building ‘software-permissions.Rmd’ SUMMARY: processing the following files failed: ‘cfr.Rmd’ ‘delay_distributions.Rmd’ ‘estimate_ascertainment.Rmd’ ‘estimate_static_severity.Rmd’ ‘estimate_time_varying_severity.Rmd’ Error: Vignette re-building failed. Execution halted Package: cfr Check: tests New result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [3s/3s] 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) > library(cfr) > > test_check("cfr") `cfr_rolling()` is a convenience function to help understand how additional data influences the overall (static) severity. Use `cfr_time_varying()` instead to estimate severity changes over the course of the outbreak. Total deaths = 99 and expected outcomes = 0 so setting expected outcomes = NA. If we were to assume total deaths = expected outcomes, it would produce an estimate of 1. [ FAIL 11 | WARN 1 | SKIP 4 | PASS 34 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (4): 'test-estimate_outcomes.R:46:3', 'test-estimate_severity.R:47:3', 'test-prepare_data.R:35:3', 'test-prepare_data.R:126:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-delay_density.R:9:3'): CFR functions work with delay_density as lambda ── Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated Backtrace: ▆ 1. ├─testthat::expect_no_warning(cfr_static(ebola1976, delay_density = ddens)) at test-delay_density.R:9:3 2. │ └─testthat:::expect_no_(...) 3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─rlang::try_fetch(...) 6. │ │ └─base::withCallingHandlers(...) 7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 8. └─cfr::cfr_static(ebola1976, delay_density = ddens) 9. └─base::stopifnot(...) ── Error ('test-delay_density.R:34:3'): CFR functions work with delay_density as ── Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated Backtrace: ▆ 1. ├─testthat::expect_no_warning(cfr_static(ebola1976, delay_density = ddens)) at test-delay_density.R:34:3 2. │ └─testthat:::expect_no_(...) 3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─rlang::try_fetch(...) 6. │ │ └─base::withCallingHandlers(...) 7. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 8. └─cfr::cfr_static(ebola1976, delay_density = ddens) 9. └─base::stopifnot(...) ── Error ('test-delay_density.R:59:3'): Input checking on delay_density works ── Error in `cfr_static(ebola1976, delay_density = ddens)`: Input data must have sequential dates with none missing or duplicated Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-delay_density.R:59:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─cfr::cfr_static(ebola1976, delay_density = ddens) 8. └─base::stopifnot(...) ── Error ('test-estimate_ascertainment.R:10:3'): Basic expectations for static ascertainment ── Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated Backtrace: ▆ 1. └─cfr::estimate_ascertainment(data = ebola1976, severity_baseline = 0.7) at test-estimate_ascertainment.R:10:3 2. └─cfr::cfr_static(data, delay_density = delay_density) 3. └─base::stopifnot(...) ── Error ('test-estimate_ascertainment.R:40:3'): Correct for delays for static ascertainment ── Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated Backtrace: ▆ 1. └─cfr::estimate_ascertainment(...) at test-estimate_ascertainment.R:40:3 2. └─cfr::cfr_static(data, delay_density = delay_density) 3. └─base::stopifnot(...) ── Error ('test-estimate_ascertainment.R:81:3'): Static ascertainment from vignette ── Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated Backtrace: ▆ 1. └─testthat::expect_snapshot(...) at test-estimate_ascertainment.R:81:3 2. └─rlang::cnd_signal(state$error) ── Error ('test-estimate_ascertainment.R:94:3'): Ascertainment > 1.0 throws a warning ── Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-estimate_ascertainment.R:94:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─cfr::estimate_ascertainment(...) 8. └─cfr::cfr_static(data, delay_density = delay_density) 9. └─base::stopifnot(...) ── Error ('test-estimate_ascertainment.R:119:3'): Ascertainment is statistically correct ── Error in `cfr_static(data, delay_density = delay_density)`: Input data must have sequential dates with none missing or duplicated Backtrace: ▆ 1. ├─testthat::expect_identical(...) at test-estimate_ascertainment.R:119:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─cfr::estimate_ascertainment(data, severity_baseline = 0.01) 5. └─cfr::cfr_static(data, delay_density = delay_density) 6. └─base::stopifnot(...) ── Error ('test-estimate_rolling.R:8:1'): (code run outside of `test_that()`) ── Error in `cfr_rolling(data = ebola1976)`: Input data must have sequential dates with none missing or duplicated Backtrace: ▆ 1. └─cfr::cfr_rolling(data = ebola1976) at test-estimate_rolling.R:8:1 2. └─base::stopifnot(...) ── Error ('test-estimate_static.R:11:1'): (code run outside of `test_that()`) ── Error in `cfr_static(data = ebola1976)`: Input data must have sequential dates with none missing or duplicated Backtrace: ▆ 1. └─cfr::cfr_static(data = ebola1976) at test-estimate_static.R:11:1 2. └─base::stopifnot(...) ── Error ('test-estimate_time_varying.R:11:1'): (code run outside of `test_that()`) ── Error in `cfr_time_varying(ebola1976)`: Input data must have sequential dates with none missing or duplicated Backtrace: ▆ 1. └─cfr::cfr_time_varying(ebola1976) at test-estimate_time_varying.R:11:1 2. └─base::stopifnot(...) [ FAIL 11 | WARN 1 | SKIP 4 | PASS 34 ] Error: Test failures Execution halted Package: dibble Check: tests New result: ERROR Running ‘testthat.R’ [4s/4s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(dibble) Attaching package: 'dibble' The following object is masked from 'package:stats': filter The following objects are masked from 'package:base': apply, colnames, diag, diag<-, ifelse, ncol, nrow, pmax, pmin, rownames > > test_check("dibble") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 181 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-dim_names.R:15:3'): dim_names ──────────────────────────────── intersect_dim_names(list(dimnames(x), dimnames(y))) (`actual`) not equal to list(axis1 = letters[2], axis2 = tibble::tibble(col1 = 2:3, col2 = 3:4)) (`expected`). `actual` is length 3 `expected` is length 2 `names(actual)`: "axis1" "axis2" "axis3" `names(expected)`: "axis1" "axis2" `actual$axis3` is a character vector () `expected$axis3` is absent [ FAIL 1 | WARN 0 | SKIP 0 | PASS 181 ] Error: Test failures Execution halted Package: meteoland Check: examples New result: ERROR Running examples in ‘meteoland-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: create_meteo_interpolator > ### Title: Meteoland interpolator creation > ### Aliases: create_meteo_interpolator > > ### ** Examples > > > # example meteo data > data(meteoland_meteo_example) > > # create the interpolator with default params > with_meteo(meteoland_meteo_example) |> + create_meteo_interpolator() ℹ Checking meteorology object... ✔ meteorology object ok ℹ Creating interpolator... Warning: No interpolation parameters provided, using defaults ℹ Set the `params` argument to modify parameter default values Error in `/.difftime`(diff(range(ud)), mean(ud)) : second argument of / cannot be a "difftime" object Calls: create_meteo_interpolator ... -> regular_intervals -> isTRUE -> /.difftime Execution halted Package: meteoland Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘reshaping-meteo.Rmd’ using rmarkdown Quitting from lines 140-143 [raster_meteo_preparing] (reshaping-meteo.Rmd) Error: processing vignette 'reshaping-meteo.Rmd' failed with diagnostics: second argument of / cannot be a "difftime" object --- failed re-building ‘reshaping-meteo.Rmd’ --- re-building ‘tidy-meteoland.Rmd’ using rmarkdown Quitting from lines 118-126 [quick_interpolation] (tidy-meteoland.Rmd) Error: processing vignette 'tidy-meteoland.Rmd' failed with diagnostics: second argument of / cannot be a "difftime" object --- failed re-building ‘tidy-meteoland.Rmd’ SUMMARY: processing the following files failed: ‘reshaping-meteo.Rmd’ ‘tidy-meteoland.Rmd’ Error: Vignette re-building failed. Execution halted Package: meteoland Check: tests New result: ERROR Running ‘testthat.R’ [139s/109s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(meteoland) Package 'meteoland' [ver. 2.2.3] > > test_check("meteoland") Starting 2 test processes [ FAIL 8 | WARN 0 | SKIP 0 | PASS 333 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-03_interpolator_object.R:11:3'): create_meteo_interpolator works as expected ── Error in ``/.difftime`(diff(range(ud)), mean(ud))`: second argument of / cannot be a "difftime" object Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-03_interpolator_object.R:11:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─meteoland::create_meteo_interpolator(meteo_test_correct, params = list(debig = FALSE)) 8. ├─stars::st_dimensions(date = dates, station = stations) 9. └─stars:::st_dimensions.default(date = dates, station = stations) 10. ├─stars:::create_dimensions(...) 11. └─base::mapply(...) 12. └─stars (local) ``(...) 13. └─stars:::regular_intervals(values) 14. ├─base::isTRUE(as.numeric(abs(diff(range(ud))/mean(ud))) < epsilon) 15. └─base::`/.difftime`(diff(range(ud)), mean(ud)) ── Error ('test-03_interpolator_object.R:161:1'): (code run outside of `test_that()`) ── Error in ``/.difftime`(diff(range(ud)), mean(ud))`: second argument of / cannot be a "difftime" object Backtrace: ▆ 1. ├─base::suppressWarnings(interpolator_test <- create_meteo_interpolator(meteo_test_correct)) at test-03_interpolator_object.R:161:1 2. │ └─base::withCallingHandlers(...) 3. └─meteoland::create_meteo_interpolator(meteo_test_correct) 4. ├─stars::st_dimensions(date = dates, station = stations) 5. └─stars:::st_dimensions.default(date = dates, station = stations) 6. ├─stars:::create_dimensions(...) 7. └─base::mapply(...) 8. └─stars (local) ``(...) 9. └─stars:::regular_intervals(values) 10. ├─base::isTRUE(as.numeric(abs(diff(range(ud))/mean(ud))) < epsilon) 11. └─base::`/.difftime`(diff(range(ud)), mean(ud)) ── Error ('test-04_interpolation_framework.R:62:3'): interpolation process works as intended ── Error in `dplyr::mutate(dplyr::as_tibble(spatial_data), interpolated_data = res_list)`: i In argument: `interpolated_data = res_list`. Caused by error in `/.difftime`: ! second argument of / cannot be a "difftime" object Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-04_interpolation_framework.R:62:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─meteoland::interpolate_data(...) 8. │ ├─meteoland:::.binding_interpolation_results(...) 9. │ │ ├─sf::st_as_sf(dplyr::mutate(dplyr::as_tibble(spatial_data), interpolated_data = res_list)) 10. │ │ ├─dplyr::mutate(dplyr::as_tibble(spatial_data), interpolated_data = res_list) 11. │ │ └─dplyr:::mutate.data.frame(dplyr::as_tibble(spatial_data), interpolated_data = res_list) 12. │ │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) 13. │ │ ├─base::withCallingHandlers(...) 14. │ │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns) 15. │ │ └─mask$eval_all_mutate(quo) 16. │ │ └─dplyr (local) eval() 17. │ └─meteoland:::.interpolation_spatial_dispatcher(...) 18. │ └─meteoland:::.interpolation_point(...) 19. │ ├─dplyr::filter(interpolator, as.Date(date) %in% as.Date(dates)) 20. │ └─stars:::filter.stars(interpolator, as.Date(date) %in% as.Date(dates)) 21. │ ├─stars::st_as_stars(cb$mets, dimensions = get_dims(cb$dims, st_dimensions(.data))) 22. │ ├─stars:::st_as_stars.list(...) 23. │ └─stars:::get_dims(cb$dims, st_dimensions(.data)) 24. │ └─stars:::create_dimension(...) 25. │ └─stars:::regular_intervals(values) 26. │ ├─base::isTRUE(as.numeric(abs(diff(range(ud))/mean(ud))) < epsilon) 27. │ └─base::`/.difftime`(diff(range(ud)), mean(ud)) 28. │ └─base::stop("second argument of / cannot be a \"difftime\" object") 29. └─base::.handleSimpleError(...) 30. └─dplyr (local) h(simpleError(msg, call)) 31. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) ── Error ('test-04_interpolation_framework.R:447:3'): interpolation cross validation works as expected ── Error in `purrr::map(stations, .station_cross_validation, interpolator = interpolator, .progress = verbose)`: i In index: 1. Caused by error in `/.difftime`: ! second argument of / cannot be a "difftime" object Backtrace: ▆ 1. ├─testthat::expect_type(...) at test-04_interpolation_framework.R:447:3 2. │ └─testthat::quasi_label(enquo(object), arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─meteoland::interpolation_cross_validation(meteoland_interpolator_example) 5. │ ├─meteoland:::.set_predicted_nas(...) 6. │ ├─purrr::list_rbind(...) 7. │ │ └─purrr:::check_list_of_data_frames(x) 8. │ │ └─vctrs::obj_check_list(x, call = error_call) 9. │ └─purrr::map(...) 10. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 11. │ ├─purrr:::with_indexed_errors(...) 12. │ │ └─base::withCallingHandlers(...) 13. │ ├─purrr:::call_with_cleanup(...) 14. │ └─meteoland (local) .f(.x[[i]], ...) 15. │ ├─dplyr::rename(...) 16. │ ├─dplyr::mutate(...) 17. │ ├─base::suppressMessages(...) 18. │ │ └─base::withCallingHandlers(...) 19. │ ├─base::suppressWarnings(...) 20. │ │ └─base::withCallingHandlers(...) 21. │ └─meteoland:::.interpolation_point(...) 22. │ ├─dplyr::filter(interpolator, as.Date(date) %in% as.Date(dates)) 23. │ └─stars:::filter.stars(interpolator, as.Date(date) %in% as.Date(dates)) 24. │ ├─stars::st_as_stars(cb$mets, dimensions = get_dims(cb$dims, st_dimensions(.data))) 25. │ ├─stars:::st_as_stars.list(...) 26. │ └─stars:::get_dims(cb$dims, st_dimensions(.data)) 27. │ └─stars:::create_dimension(...) 28. │ └─stars:::regular_intervals(values) 29. │ ├─base::isTRUE(as.numeric(abs(diff(range(ud))/mean(ud))) < epsilon) 30. │ └─base::`/.difftime`(diff(range(ud)), mean(ud)) 31. │ └─base::stop("second argument of / cannot be a \"difftime\" object") 32. └─base::.handleSimpleError(...) 33. └─purrr (local) h(simpleError(msg, call)) 34. └─cli::cli_abort(...) 35. └─rlang::abort(...) ── Error ('test-05_summary_interpolated_data.R:2:3'): summarise_interpolated_data for sf works as expected ── Error in `dplyr::mutate(dplyr::as_tibble(spatial_data), interpolated_data = res_list)`: i In argument: `interpolated_data = res_list`. Caused by error in `/.difftime`: ! second argument of / cannot be a "difftime" object Backtrace: ▆ 1. ├─meteoland::interpolate_data(...) at test-05_summary_interpolated_data.R:2:3 2. │ ├─meteoland:::.binding_interpolation_results(...) 3. │ │ ├─sf::st_as_sf(dplyr::mutate(dplyr::as_tibble(spatial_data), interpolated_data = res_list)) 4. │ │ ├─dplyr::mutate(dplyr::as_tibble(spatial_data), interpolated_data = res_list) 5. │ │ └─dplyr:::mutate.data.frame(dplyr::as_tibble(spatial_data), interpolated_data = res_list) 6. │ │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) 7. │ │ ├─base::withCallingHandlers(...) 8. │ │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns) 9. │ │ └─mask$eval_all_mutate(quo) 10. │ │ └─dplyr (local) eval() 11. │ └─meteoland:::.interpolation_spatial_dispatcher(...) 12. │ └─meteoland:::.interpolation_point(...) 13. │ ├─dplyr::filter(interpolator, as.Date(date) %in% as.Date(dates)) 14. │ └─stars:::filter.stars(interpolator, as.Date(date) %in% as.Date(dates)) 15. │ ├─stars::st_as_stars(cb$mets, dimensions = get_dims(cb$dims, st_dimensions(.data))) 16. │ ├─stars:::st_as_stars.list(...) 17. │ └─stars:::get_dims(cb$dims, st_dimensions(.data)) 18. │ └─stars:::create_dimension(...) 19. │ └─stars:::regular_intervals(values) 20. │ ├─base::isTRUE(as.numeric(abs(diff(range(ud))/mean(ud))) < epsilon) 21. │ └─base::`/.difftime`(diff(range(ud)), mean(ud)) 22. │ └─base::stop("second argument of / cannot be a \"difftime\" object") 23. └─base::.handleSimpleError(...) 24. └─dplyr (local) h(simpleError(msg, call)) 25. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) ── Error ('test-05_summary_interpolated_data.R:225:3'): summarise_interpolated_data for stars works as expected ── Error in ``/.difftime`(diff(range(ud)), mean(ud))`: second argument of / cannot be a "difftime" object Backtrace: ▆ 1. └─meteoland::interpolate_data(...) at test-05_summary_interpolated_data.R:225:3 2. ├─meteoland:::.binding_interpolation_results(...) 3. │ ├─stars::st_dimensions(...) 4. │ └─stars:::st_dimensions.default(...) 5. └─meteoland:::.interpolation_spatial_dispatcher(...) 6. └─meteoland:::.interpolation_point(...) 7. ├─dplyr::filter(interpolator, as.Date(date) %in% as.Date(dates)) 8. └─stars:::filter.stars(interpolator, as.Date(date) %in% as.Date(dates)) 9. ├─stars::st_as_stars(cb$mets, dimensions = get_dims(cb$dims, st_dimensions(.data))) 10. ├─stars:::st_as_stars.list(...) 11. └─stars:::get_dims(cb$dims, st_dimensions(.data)) 12. └─stars:::create_dimension(...) 13. └─stars:::regular_intervals(values) 14. ├─base::isTRUE(as.numeric(abs(diff(range(ud))/mean(ud))) < epsilon) 15. └─base::`/.difftime`(diff(range(ud)), mean(ud)) ── Error ('test-05_summary_interpolated_data.R:381:3'): summarise_interpolator works as expected ── Error in ``/.difftime`(diff(range(ud)), mean(ud))`: second argument of / cannot be a "difftime" object Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-05_summary_interpolated_data.R:381:3 2. │ └─testthat:::expect_condition_matching(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. ├─meteoland::summarise_interpolator(...) 8. │ ├─assertthat::assert_that(.is_interpolator(interpolator)) 9. │ │ └─assertthat::see_if(..., env = env, msg = msg) 10. │ │ ├─base::tryCatch(...) 11. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 12. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 13. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 14. │ │ └─base::eval(assertion, env) 15. │ │ └─base::eval(assertion, env) 16. │ └─meteoland:::.is_interpolator(interpolator) 17. │ └─meteoland::get_interpolation_params(interpolator) 18. └─meteoland::interpolate_data(...) 19. ├─meteoland:::.binding_interpolation_results(...) 20. │ ├─stars::st_dimensions(...) 21. │ └─stars:::st_dimensions.default(...) 22. └─meteoland:::.interpolation_spatial_dispatcher(...) 23. └─meteoland:::.interpolation_point(...) 24. ├─dplyr::filter(interpolator, as.Date(date) %in% as.Date(dates)) 25. └─stars:::filter.stars(interpolator, as.Date(date) %in% as.Date(dates)) 26. ├─stars::st_as_stars(cb$mets, dimensions = get_dims(cb$dims, st_dimensions(.data))) 27. ├─stars:::st_as_stars.list(...) 28. └─stars:::get_dims(cb$dims, st_dimensions(.data)) 29. └─stars:::create_dimension(...) 30. └─stars:::regular_intervals(values) 31. ├─base::isTRUE(as.numeric(abs(diff(range(ud))/mean(ud))) < epsilon) 32. └─base::`/.difftime`(diff(range(ud)), mean(ud)) ── Error ('test-21_meteoland_utils.R:293:3'): precipitation_rainfall_erosivity works as expected ── Error in `dplyr::mutate(dplyr::as_tibble(spatial_data), interpolated_data = res_list)`: i In argument: `interpolated_data = res_list`. Caused by error in `/.difftime`: ! second argument of / cannot be a "difftime" object Backtrace: ▆ 1. ├─testthat::expect_s3_class(...) at test-21_meteoland_utils.R:293:3 2. │ └─testthat::quasi_label(enquo(object), arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─dplyr::mutate(...) 5. ├─meteoland::interpolate_data(...) 6. │ ├─meteoland:::.binding_interpolation_results(...) 7. │ │ ├─sf::st_as_sf(dplyr::mutate(dplyr::as_tibble(spatial_data), interpolated_data = res_list)) 8. │ │ ├─dplyr::mutate(dplyr::as_tibble(spatial_data), interpolated_data = res_list) 9. │ │ └─dplyr:::mutate.data.frame(dplyr::as_tibble(spatial_data), interpolated_data = res_list) 10. │ │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) 11. │ │ ├─base::withCallingHandlers(...) 12. │ │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns) 13. │ │ └─mask$eval_all_mutate(quo) 14. │ │ └─dplyr (local) eval() 15. │ └─meteoland:::.interpolation_spatial_dispatcher(...) 16. │ └─meteoland:::.interpolation_point(...) 17. │ ├─dplyr::filter(interpolator, as.Date(date) %in% as.Date(dates)) 18. │ └─stars:::filter.stars(interpolator, as.Date(date) %in% as.Date(dates)) 19. │ ├─stars::st_as_stars(cb$mets, dimensions = get_dims(cb$dims, st_dimensions(.data))) 20. │ ├─stars:::st_as_stars.list(...) 21. │ └─stars:::get_dims(cb$dims, st_dimensions(.data)) 22. │ └─stars:::create_dimension(...) 23. │ └─stars:::regular_intervals(values) 24. │ ├─base::isTRUE(as.numeric(abs(diff(range(ud))/mean(ud))) < epsilon) 25. │ └─base::`/.difftime`(diff(range(ud)), mean(ud)) 26. │ └─base::stop("second argument of / cannot be a \"difftime\" object") 27. └─base::.handleSimpleError(...) 28. └─dplyr (local) h(simpleError(msg, call)) 29. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) [ FAIL 8 | WARN 0 | SKIP 0 | PASS 333 ] Error: Test failures Execution halted Package: phenofit Check: tests New result: ERROR Running ‘testthat.R’ [57s/57s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(phenofit) > > test_check("phenofit") List of 5 $ AG : tibble [6 × 8] (S3: tbl_df/tbl/data.frame) $ Beck : tibble [6 × 7] (S3: tbl_df/tbl/data.frame) $ Elmore: tibble [6 × 8] (S3: tbl_df/tbl/data.frame) $ Gu : tibble [6 × 10] (S3: tbl_df/tbl/data.frame) $ Zhang : tibble [6 × 8] (S3: tbl_df/tbl/data.frame) NULL # A tibble: 6 × 8 flag t0 mn mx rsp a3 rau a5 1 1999_1 -135. 0.201 0.636 0.00932 2.85 0.00852 2 2 2000_1 189. 0.238 0.635 0.0126 2.47 0.00801 3.21 3 2001_1 569. 0.252 0.626 0.0108 2.96 0.00950 2.96 4 2002_1 892. 0.253 0.614 0.0159 2 0.00724 3.08 5 2003_1 1268. 0.236 0.577 0.0121 2.88 0.00723 2.88 6 2004_1 1677. 0.202 0.576 0.00832 2.84 0.00990 3.48 meth R2 NSE R RMSE pvalue n_sim 1: AG 0.9986908 0.9985845 0.9993452 9.940385e-03 4.489925e-65 46 2: Beck 1.0000000 1.0000000 1.0000000 1.389780e-09 0.000000e+00 46 3: Elmore 1.0000000 1.0000000 1.0000000 4.161813e-10 0.000000e+00 46 4: Gu 1.0000000 1.0000000 1.0000000 4.891365e-11 0.000000e+00 46 5: Zhang 1.0000000 1.0000000 1.0000000 5.529073e-06 8.043461e-208 46 $AG formula: mn + (mx - mn) * exp(-((t0 - t) * rsp)^a3) formula: mn + (mx - mn) * exp(-((t - t0) * rau)^a5) pars: t0 mn mx rsp a3 rau a5 nlminb 149.8926 0.1020656 0.7095242 0.009389263 6 0.009367765 6 warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.65502e-16); attempting approx solution warning: solve(): system is singular (rcond: 2.19427e-17); attempting approx solution warning: solve(): system is singular (rcond: 1.65502e-16); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.33432e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.03034e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.33432e-17); attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.08395e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.36432e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 6.97437e-18); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.80681e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular (rcond: 3.05447e-17); attempting approx solution warning: solve(): system is singular (rcond: 2.11109e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 6.04329e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.80681e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.94249e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.84957e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 8.58712e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.09346e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.82199e-17); attempting approx solution warning: solve(): system is singular (rcond: 2.38705e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 5.88785e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.85037e-16); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 7.40149e-17); attempting approx solution warning: solve(): system is singular (rcond: 6.20634e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 2.38811e-17); attempting approx solution warning: solve(): system is singular (rcond: 3.05447e-17); attempting approx solution warning: solve(): system is singular (rcond: 2.11109e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 5.43896e-17); attempting approx solution warning: solve(): system is singular (rcond: 4.38854e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.00786e-16); attempting approx solution warning: solve(): system is singular (rcond: 1.46031e-17); attempting approx solution warning: solve(): system is singular (rcond: 5.02097e-17); attempting approx solution warning: solve(): system is singular (rcond: 1.25524e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 3.31005e-17); attempting approx solution [ FAIL 1 | WARN 2 | SKIP 0 | PASS 69 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-curvefit.R:18:5'): curvefit works ──────────────────────────── all.equal(p1, p2, tolerance = 1e-06) is not TRUE `actual` is a character vector ('Component "Elmore": Component "mn": Mean relative difference: 1.990404e-06') `expected` is a logical vector (TRUE) [ FAIL 1 | WARN 2 | SKIP 0 | PASS 69 ] Error: Test failures Execution halted