Running ‘testthat.R’ [93s/133s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Had the same issue as in this thread: https://github.com/hadley/testthat/issues/86
  > Sys.setenv("R_TESTS" = "")
  > 
  > options(deparse.max.lines = 5)
  > suppressWarnings(RNGversion("3.5.0"))
  > 
  > testthat::test_check("dynamichazard", reporter = "summary")
  Loading required package: dynamichazard
  Loading required package: survival
  Tracing function "expect_known_value" in package "testthat"
  Tracing function "expect_known_output" in package "testthat"
  Loading required package: DBI
  Running tests for GMA: ..................
  Testing LAPACK wrapper functions: ..............................................
  Running test_PF: ........................................................................................................................................................................................................SS...SSSSSSSS..S12SS..SSSSSSSSS
  Testing SMA: ................................
  Testing UKF: .........................
  Testing bigglm_wrapper: ..........
  Testing boot: ...S..................................................................................................................................................................................................................................................................................................................................................................................................................
  testing cloglog link function: ....S
  Testing cpp sampling functions: ..................................................................................................................................................................................................................................................................................................................................................................................................................S.............................................................S....
  Running test_cpp_utils.R:: .S............
  Testing ddhazard w/ generic things and w/ the the EKF : .....................S................
  Testing design_mat_and_risk_obj: ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
  Testing fixed_effects_in_E_step: .........
  Testing test_fixed_effects_in_M_step: ..........S..
  Testing 'get_start_values': ....................
  Running tests for hatvalues: ....
  Testing examples in man files: .......S.S....SSSS........S
  Testing loglike: ........................
  Testing options: .
  Testing parallelglm vs. glm: ................................................S
  Testing plot functions: ......................................
  Testing predict: ...............................................................................SS
  Testing print function: ...SS.....
  Testing residuals functions: ..................................................................................................................................................................................................SS
  Testing shiny app: ..
  Testing static_glm: .............................
  Testing summary function: .................
  Testing test_utils: ............S......................................
  Testing weights in fit: ................
  
  ══ Skipped ═════════════════════════════════════════════════════════════════════
  1. PF_smooth gives same results (@test_PF.R#71) - On CRAN
  
  2. Import and export PF cloud from Rcpp gives the same (@test_PF.R#249) - On CRAN
  
  3. PF_EM gives previous results on head neck data set (@test_PF.R#342) - On CRAN
  
  4. PF_EM gives previous results on head neck data set with fixed effects and the logit model (@test_PF.R#409) - On CRAN
  
  5. compute_PF_summary_stats gives previous results (@test_PF.R#434) - On CRAN
  
  6. 'get_cloud_means' and 'get_cloud_quantiles' gives previous results (@test_PF.R#508) - On CRAN
  
  7. 'get_ancestors' yields the correct result (@test_PF.R#558) - On CRAN
  
  8. ´est_params_dens´ gives the same as a R version (@test_PF.R#580) - On CRAN
  
  9. fixed effect estimation gives the same as an R implementation (@test_PF.R#628) - On CRAN
  
  10. A few iterations with `type = "VAR"' yields the same as before (@test_PF.R#709) - On CRAN
  
  11. PF_EM gives the same with restricted and unrestricted model when we estimate all the parameters (@test_PF.R#778) - On CRAN
  
  12. Using `n_smooth_final` works as expected and yields previous results (@test_PF.R#883) - On CRAN
  
  13. sampling with a t-distribution gives previous results (@test_PF.R#949) - On CRAN
  
  14. 'PF_forward_filter' gives the same as 'PF_EM' when it should (@test_PF.R#987) - On CRAN
  
  15. 'state_fw' gives correct results (@test_PF.R#1116) - !dir.exists("pf-internals")
  
  16. 'state_bw' gives correct results (@test_PF.R#1152) - !dir.exists("pf-internals")
  
  17. 'artificial_prior' gives correct results (@test_PF.R#1187) - !dir.exists("pf-internals")
  
  18. 'observational_cdist' gives correct results (@test_PF.R#1221) - !dir.exists("pf-internals")
  
  19. combining forward and backwards works (@test_PF.R#1266) - !dir.exists("pf-internals")
  
  20. combining prior and backwards works (@test_PF.R#1313) - !dir.exists("pf-internals")
  
  21. mode approximations give expected result (@test_PF.R#1351) - !dir.exists("pf-internals")
  
  22. 'PF_get_score_n_hess' gives the same as an R implementation (@test_PF.R#1493) - On CRAN
  
  23. boot yields previously computed values with pbc (@test_boot_est.R#19) - On CRAN
  
  24. cloglog function gives previous result with simulated data using PF_EM and PF_forward_filter (@test_cloglog.R#56) - On CRAN
  
  25. mvrnorm gives expected sample mean and variance (@test_cpp_sample_funcs.R#50) - On CRAN
  
  26. 'mvtrnorm' yields close to uniform sample (@test_cpp_sample_funcs.R#111) - On CRAN
  
  27. trunc_lp_in_exponential_dist does not truncate when not needed (@test_cpp_utils.R#12) - On CRAN
  
  28. Different non-integer time_scales gives the same result with ddhazard (@test_ddhazard_n_EKF.R#165) - On CRAN
  
  29. posterior_approx gives previous found values with fixed effects in M-step (@test_fixed_effects_in_M_step.R#187) - On CRAN
  
  30. residuals.ddhazard help page examples gives the same results (@test_help_page_examples.R#43) - On CRAN
  
  31. ddhazard_boot help page examples gives the same results (@test_help_page_examples.R#67) - On CRAN
  
  32. PF_EM help page example runs and gives previous computed results (@test_help_page_examples.R#129) - On CRAN
  
  33. Second example on PF help page gives the same result (@test_help_page_examples.R#170) - On CRAN
  
  34. example in 'PF_EM' with gives previous results w/ a few iterations (@test_help_page_examples.R#226) - On CRAN
  
  35. `PF_forward_filter` the results stated in the comments and does not alter the .Random.seed as stated on the help page (@test_help_page_examples.R#357) - On CRAN
  
  36. 'PF_get_score_n_hess' gives previous results (@test_help_page_examples.R#515) - On CRAN
  
  37. glm and parallelglm gives the same (@test_parallelglm.R#80) - On CRAN
  
  38. Terms from predict with exponential outcome are correct (@test_predict.R#413) - On CRAN
  
  39. Different non-integer time_scales gives the same result with predict results (@test_predict.R#474) - On CRAN
  
  40. print.ddhazard_boot gives the expected output (@test_print.R#39) - On CRAN
  
  41. Print function for PF objects gives previous results (@test_print.R#89) - On CRAN
  
  42. Gets previous results with Rossi (@test_residuals.R#209) - On CRAN
  
  43. Get prevoius residuals with whas500 (@test_residuals.R#236) - On CRAN
  
  44. Testing util functions to sim series for tests (@test_test_utils.R#28) - On CRAN
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Failure: type = 'VAR' works with non-zero mean with a single term and give
  pf_Fear[!names(pf_Fear) %in% "clouds"] has changed from known value recorded in './previous_results/PF_VARS_non_zero_mean_inter.RDS'.
  Component "fixed_effects": Mean relative difference: 0.0001439805
  Component "Q": Mean relative difference: 0.00548708
  Component "F": Mean relative difference: 0.007264776
  Component "EM_ests": Component "fixed_effects": Mean relative difference: 0.0001451387
  Component "EM_ests": Component "F": Mean relative difference: 0.007114569
  Component "EM_ests": Component "Q": Mean relative difference: 0.003421887
  Component "log_likes": Mean relative difference: 1.515183e-05
  Component "effective_sample_size": Component "forward_clouds": Mean relative difference: 0.0001972975
  Component "effective_sample_size": Component "backward_clouds": Mean relative difference: 0.001554409
  ...
  
  ── 2. Failure: type = 'VAR' works with non-zero mean with a single term and give
  pf_Fear[!names(pf_Fear) %in% "clouds"] has changed from known value recorded in './previous_results/PF_VARS_non_zero_mean_slope.RDS'.
  Component "fixed_effects": Mean relative difference: 0.0004245941
  Component "Q": Mean relative difference: 0.002155951
  Component "F": Mean relative difference: 0.02190669
  Component "EM_ests": Component "fixed_effects": Mean relative difference: 0.0002310787
  Component "EM_ests": Component "F": Mean relative difference: 0.07697142
  Component "EM_ests": Component "Q": Mean relative difference: 0.001386713
  Component "log_likes": Mean relative difference: 8.368518e-07
  Component "effective_sample_size": Component "forward_clouds": Mean relative difference: 0.0002168266
  Component "effective_sample_size": Component "backward_clouds": Mean relative difference: 0.03617261
  ...
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted