* using log directory 'd:/Rcompile/CRANpkg/local/4.5/cfr.Rcheck'
* using R Under development (unstable) (2025-02-11 r87713 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'cfr/DESCRIPTION' ... OK
* this is package 'cfr' version '0.1.2'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'cfr' can be installed ... OK
* 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] OK
* checking whether the package can be loaded with stated dependencies ... [0s] OK
* checking whether the package can be unloaded cleanly ... [0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s] OK
* checking loading without being on the library search path ... [0s] OK
* checking use of S3 registration ... 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 ... [2s] OK
* checking Rd files ... [1s] 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 ... [1s] 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 ... [0s] 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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [5s] 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [14s] 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

* checking PDF version of manual ... [20s] OK
* checking HTML version of manual ... [3s] OK
* DONE
Status: 3 ERRORs