CRAN Package Check Results for Package cfr

Last updated on 2025-02-23 19:51:01 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.1.2	2.44	42.15	44.59	ERROR
r-devel-linux-x86_64-debian-gcc	0.2.0	1.75	77.82	79.57	OK
r-devel-linux-x86_64-fedora-clang	0.2.0			170.41	OK
r-devel-linux-x86_64-fedora-gcc	0.2.0			190.87	OK
r-devel-macos-arm64	0.1.2			84.00	OK
r-devel-macos-x86_64	0.2.0			176.00	OK
r-devel-windows-x86_64	0.1.2	5.00	65.00	70.00	ERROR
r-patched-linux-x86_64	0.1.2	2.62	90.23	92.85	OK
r-release-linux-x86_64	0.2.0	2.12	94.62	96.74	OK
r-release-macos-arm64	0.1.2			91.00	OK
r-release-macos-x86_64	0.2.0			209.00	OK
r-release-windows-x86_64	0.1.2	3.00	154.00	157.00	OK
r-oldrel-macos-arm64	0.1.2			91.00	OK
r-oldrel-macos-x86_64	0.2.0			170.00	OK
r-oldrel-windows-x86_64	0.1.2	4.00	153.00	157.00	OK

Check Details

Version: 0.1.2
Check: examples
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 Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.2
Check: tests
Result: ERROR Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [5s/5s] 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 <distcrete> ── 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 Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.2
Check: re-building of vignette outputs
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 Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.2
Check: examples
Result: ERROR Running examples in 'cfr-Ex.R' failed The error most likely occurred in: > ### 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 Flavor: r-devel-windows-x86_64

Version: 0.1.2
Check: tests
Result: ERROR Running 'spelling.R' [0s] Running 'testthat.R' [4s] 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 <distcrete> ── 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 Flavor: r-devel-windows-x86_64

Version: 0.1.2
Check: re-building of vignette outputs
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 Flavor: r-devel-windows-x86_64