Running 'testthat.R' [231s]
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:  8
  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:  8
  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 0 | WARN 0 | SKIP 0 | PASS 176 ]
  > 
  > proc.time()
     user  system elapsed 
    60.31    1.15   64.62