R Under development (unstable) (2025-12-07 r89119 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # 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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(checkmate)
> library(bayestransmission)
> 
> test_check("bayestransmission")
[ FAIL 0 | WARN 0 | SKIP 43 | PASS 294 ]

══ Skipped tests (43) ══════════════════════════════════════════════════════════
• Abstract class - tested via derived classes in other modules (1):
  'test-Module-Infect.R:47:3'
• Base class - tested via derived classes (1): 'test-Module-utils.R:6:3'
• Class CppFacility not exposed in this build (1): 'test-Module-Infect.R:29:3'
• Class CppHistoryLink not exposed in this build (1):
  'test-cpp-comparison.R:178:3'
• Class CppPatient not exposed in this build (1): 'test-Module-Infect.R:52:3'
• Class CppPatientState not exposed in this build (1):
  'test-Module-Infect.R:64:3'
• Class CppRawEventList not exposed in this build (3):
  'test-Module-Infect.R:78:3', 'test-Module-Infect.R:95:3',
  'test-Module-Infect.R:109:3'
• Class CppSampler not exposed in this build (1): 'test-Module-Infect.R:126:3'
• Class CppTestParamsAbx not exposed in this build (1):
  'test-Module-Infect.R:335:3'
• Class CppUnit not exposed in this build (1): 'test-Module-Infect.R:342:3'
• Conditional classes - availability depends on build configuration (1):
  'test-conditional-exposure.R:48:5'
• Full comparison test - set RUN_FULL_COMPARISON=1 to run (1):
  'test-cpp-comparison.R:413:3'
• LogNormalModelParams has constructor issues with default AcquisitionParams
  (1): 'test-parameter-initialization-cpp.R:382:3'
• Method UnitHeads not available: Requires ALL_CLASSES for Map access (1):
  'test-Module-Infect.R:204:3'
• Need to create standalone test - currently tested via integration (9):
  'test-Module-Infect.R:9:3', 'test-Module-Infect.R:14:3',
  'test-Module-Infect.R:19:3', 'test-Module-Infect.R:24:3',
  'test-Module-Infect.R:37:3', 'test-Module-Infect.R:42:3',
  'test-Module-lognormal.R:9:3', 'test-Module-lognormal.R:14:3',
  'test-Module-lognormal.R:19:3'
• On CRAN (5): 'test-likelihood-exact-parity.R:2:3',
  'test-likelihood-exact-parity.R:144:3',
  'test-likelihood-parity-diagnostic.R:2:3',
  'test-likelihood-parity-diagnostic.R:99:3',
  'test-likelihood-parity-diagnostic.R:201:3'
• Skipping interactive MCMC test (1): 'test-loglikelihood-components.R:89:3'
• Small numerical discrepancy (~0.3%) between R and C++ - needs investigation
  (1): 'test-cpp-comparison.R:315:3'
• Tested via SystemHistory properties (UnitHeads, PatientHeads, etc.) (1):
  'test-Module-utils.R:11:3'
• UnitHeads requires ALL_CLASSES (1): 'test-Module-lognormal.R:64:3'
• getEventList requires ALL_CLASSES (3): 'test-Module-Infect.R:214:3',
  'test-Module-Infect.R:253:3', 'test-Module-Infect.R:286:3'
• getHistoryLinkList requires ALL_CLASSES (5): 'test-cpp-comparison.R:242:3',
  'test-cpp-comparison.R:300:3', 'test-cpp-comparison.R:485:3',
  'test-event-likelihoods-simplified.R:230:3',
  'test-event-likelihoods-simplified.R:267:3'
• getPatients requires ALL_CLASSES (1):
  'test-event-likelihoods-simplified.R:116:3'

[ FAIL 0 | WARN 0 | SKIP 43 | PASS 294 ]
> 
> proc.time()
   user  system elapsed 
   9.76    0.62   10.32