Running 'testthat.R' [88s]
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(ern)
  
  ern version: 1.3.1 
  
  If not already installed, software JAGS is recommended. 
  (https://sourceforge.net/projects/mcmc-jags/files/)
  
  > 
  > test_check("ern")
  Compiling model graph
     Resolving undeclared variables
     Allocating nodes
  Graph information:
     Observed stochastic nodes: 8
     Unobserved stochastic nodes: 58
     Total graph size: 790
  
  Initializing model
  
  Wastewater data smoothed using loess method
  iterations Richardson-Lucy deconvolution:  20
  -----
  The clinical testing data you input is not daily. `ern` requires daily data to compute Rt. `ern` will infer daily reports from your inputs. See `prm.daily` and `prm.daily.check` arguments of `estimate_R_cl()` for daily inference options.
  -----
  Assuming the first observed report (from 2020-03-14)
  is aggregated over 7 previous days
  (second observation's aggregation period).
  This can be changed in `estimate_R_cl()`, using the
  `prm.daily` argument (set a value for `first.agg.period`
  in this parameter list).
  -----
  Running MCMC model to infer daily reports from aggregated reports...
  
  Compiling model graph
     Resolving undeclared variables
     Allocating nodes
  Graph information:
     Observed stochastic nodes: 8
     Unobserved stochastic nodes: 58
     Total graph size: 790
  
  Initializing model
  
  - Filtering out any daily inferred reports associated
  with inferred aggregates outside of the specified tolerance of 10%...
  Before filtering: 56 daily reports
  After filtering:  42 daily reports
  To reduce the number of observations dropped in filtering, either:
    - adjust MCMC parameters in prm.daily (burn, iter, chains) to
        improve chances of MCMC convergence,
    - increase tolerance for this check (prm.daily.check$agg.reldiff.tol)
  Using default config in `EpiEstim::estimate_R()`.
  Deconvolution reporting delays...
  iterations Richardson-Lucy deconvolution:  10
  Deconvolution incubation period...
  iterations Richardson-Lucy deconvolution:  10
  Using default config in `EpiEstim::estimate_R()`.
  Deconvolution reporting delays...
  iterations Richardson-Lucy deconvolution:  10
  Deconvolution incubation period...
  iterations Richardson-Lucy deconvolution:  10
  Deconvolution reporting delays...
  iterations Richardson-Lucy deconvolution:  10
  Deconvolution incubation period...
  iterations Richardson-Lucy deconvolution:  10
  Using default config in `EpiEstim::estimate_R()`.
  Deconvolution reporting delays...
  iterations Richardson-Lucy deconvolution:  10
  Deconvolution incubation period...
  iterations Richardson-Lucy deconvolution:  10
  Deconvolution reporting delays...
  iterations Richardson-Lucy deconvolution:  10
  Deconvolution incubation period...
  iterations Richardson-Lucy deconvolution:  10
  iterations Richardson-Lucy deconvolution:  9
  Deconvolution incubation period...
  iterations Richardson-Lucy deconvolution:  9
  Wastewater data smoothed using loess method
  Wastewater data smoothed using loess method
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  iterations Richardson-Lucy deconvolution:  9
  
  ERROR: `si_distr` must be specified in `config.EpiEstim`. ABORTING!
  Wastewater data smoothed using loess method
  Wastewater data smoothed using rollmean method
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 175 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-estimate_R_ww.R:66:3'): estimate_R_ww executes silently when silent mode is enabled ──
  Error in `dplyr::summarise(dplyr::group_by(df, date), mean = mean(mean), 
      lwr = stats::quantile(lo, probs = 0.5 - CI/2), upr = stats::quantile(hi, 
          probs = 0.5 + CI/2), .groups = "drop")`: i In argument: `lwr = stats::quantile(lo, probs = 0.5 - CI/2)`.
  i In group 1: `date = 2022-10-25`.
  Caused by error in `quantile.default()`:
  ! missing values and NaN's not allowed if 'na.rm' is FALSE
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(...) at test-estimate_R_ww.R:66:3
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. ├─ern::estimate_R_ww(...)
   10. │ └─ern:::summarise_by_date_ens(...)
   11. │   ├─dplyr::summarise(...)
   12. │   └─dplyr:::summarise.grouped_df(...)
   13. │     └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
   14. │       ├─base::withCallingHandlers(...)
   15. │       └─dplyr:::map(quosures, summarise_eval_one, mask = mask)
   16. │         └─base::lapply(.x, .f, ...)
   17. │           └─dplyr (local) FUN(X[[i]], ...)
   18. │             └─mask$eval_all_summarise(quo)
   19. │               └─dplyr (local) eval()
   20. ├─stats::quantile(lo, probs = 0.5 - CI/2)
   21. ├─stats:::quantile.default(lo, probs = 0.5 - CI/2)
   22. │ └─base::stop("missing values and NaN's not allowed if 'na.rm' is FALSE")
   23. └─base::.handleSimpleError(...)
   24.   └─dplyr (local) h(simpleError(msg, call))
   25.     └─dplyr (local) handler(cnd)
   26.       └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 175 ]
  Error: Test failures
  Execution halted