Running ‘testthat.R’ [66s/129s]
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)
  > 
  > 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: ...............W..W.
  Testing LAPACK wrapper functions: ..........................................
  Running test_PF: ........................................................................................................................................................................................................SS...SSSSSSS..S12SS..S
  Testing SMA: ........3.........45........6...
  Testing UKF: .........................
  Testing bigglm_wrapper: ..........
  Testing boot: ...S.7................................................................................................................................................................................................................................................................................................................................................................................................................
  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: ........8
  Testing test_fixed_effects_in_M_step: ..........S..
  Testing 'get_start_values': ....................
  Running tests for hatvalues: ....
  Testing examples in man files: .......S.S....SSSS.......
  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. ´est_params_dens´ gives the same as a R version (@test_PF.R#558) - On CRAN
  
  8. fixed effect estimation gives the same as an R implementation (@test_PF.R#606) - On CRAN
  
  9. A few iterations with `type = "VAR"' yields the same as before (@test_PF.R#687) - On CRAN
  
  10. PF_EM gives the same with restricted and unrestricted model when we estimate all the parameters (@test_PF.R#768) - On CRAN
  
  11. Using `n_smooth_final` works as expected and yields previous results (@test_PF.R#887) - On CRAN
  
  12. sampling with a t-distribution gives previous results (@test_PF.R#953) - On CRAN
  
  13. 'PF_forward_filter' gives the same as 'PF_EM' when it should (@test_PF.R#991) - On CRAN
  
  14. boot yields previously computed values with pbc (@test_boot_est.R#19) - On CRAN
  
  15. cloglog function gives previous result with simulated data using PF_EM and PF_forward_filter (@test_cloglog.R#56) - On CRAN
  
  16. mvrnorm gives expected sample mean and variance (@test_cpp_sample_funcs.R#50) - On CRAN
  
  17. 'mvtrnorm' yields close to uniform sample (@test_cpp_sample_funcs.R#111) - On CRAN
  
  18. trunc_lp_in_exponential_dist does not truncate when not needed (@test_cpp_utils.R#12) - On CRAN
  
  19. Different non-integer time_scales gives the same result with ddhazard (@test_ddhazard_n_EKF.R#165) - On CRAN
  
  20. posterior_approx gives previous found values with fixed effects in M-step (@test_fixed_effects_in_M_step.R#187) - On CRAN
  
  21. residuals.ddhazard help page examples gives the same results (@test_help_page_examples.R#43) - On CRAN
  
  22. ddhazard_boot help page examples gives the same results (@test_help_page_examples.R#67) - On CRAN
  
  23. PF_EM help page example runs and gives previous computed results (@test_help_page_examples.R#130) - On CRAN
  
  24. Second example on PF help page gives the same result (@test_help_page_examples.R#171) - On CRAN
  
  25. example in 'PF_EM' with gives previous results w/ a few iterations (@test_help_page_examples.R#227) - On CRAN
  
  26. `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
  
  27. glm and parallelglm gives the same (@test_parallelglm.R#80) - On CRAN
  
  28. Terms from predict with exponential outcome are correct (@test_predict.R#413) - On CRAN
  
  29. Different non-integer time_scales gives the same result with predict results (@test_predict.R#474) - On CRAN
  
  30. print.ddhazard_boot gives the expected output (@test_print.R#39) - On CRAN
  
  31. Print function for PF objects gives previous results (@test_print.R#89) - On CRAN
  
  32. Gets previous results with Rossi (@test_residuals.R#209) - On CRAN
  
  33. Get prevoius residuals with whas500 (@test_residuals.R#236) - On CRAN
  
  34. Testing util functions to sim series for tests (@test_test_utils.R#28) - On CRAN
  
  ══ Warnings ════════════════════════════════════════════════════════════════════
  1. GAM works w/ weights (@test_GMA.R#157) - EM algorithm did not converge within the n_max number of iterations
  
  2. GAM works w/ weights (@test_GMA.R#168) - EM algorithm did not converge within the n_max number of iterations
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Failure: type = 'VAR' works with non-zero mean for with a single term and 
  pf_Fear[!names(pf_Fear) %in% "clouds"] has changed from known value recorded in './previous_results/PF_VARS_non_zero_mean_inter.RDS'.
  Component "seed": Mean relative difference: 0.9612612
  
  ── 2. Failure: type = 'VAR' works with non-zero mean for with a single term and 
  pf_Fear[!names(pf_Fear) %in% "clouds"] has changed from known value recorded in './previous_results/PF_VARS_non_zero_mean_slope.RDS'.
  Component "seed": Mean relative difference: 0.9612612
  
  ── 3. Failure: Logit model for posterior_approx gives previous found values (@te
  `f1` has changed from known value recorded in './previous_results/posterior_approx_logit_pbc.RDS'.
  Component "state_vecs": Mean relative difference: 0.07955711
  Component "state_vecs": Mean relative difference: 0.07955711
  
  ── 4. Failure: Second order model gives previous found result for posterior appr
  `f1` not equal to read_to_test("posterior_approx_logit_2_order").
  Component "state_vecs": Mean relative difference: 0.02338442
  Component "state_vecs": Mean relative difference: 0.02338442
  
  ── 5. Failure: Posterior gives previous found results with large by length for p
  `f1` not equal to read_to_test("posterior_approx_logit_pbc_large_by").
  Component "state_vecs": Mean relative difference: 0.07707501
  Component "state_vecs": Mean relative difference: 0.07707501
  
  ── 6. Failure: Exponential model for posterior_approx gives previous found value
  `f1` not equal to read_to_test("posterior_approx_exp_pbc").
  Component "state_vecs": Mean relative difference: 0.01643999
  Component "state_vecs": Mean relative difference: 0.01643999
  
  ── 7. Failure: Boot works with posterior_approx and gives previous found results
  `tmp` not equal to read_to_test("boot_posterior_approx").
  Component "t0": Mean relative difference: 0.003497934
  Component "t": Mean relative difference: 0.4141036
  
  ── 8. Failure: posterior_approx gives previous found values with fixed effects i
  `f1` has changed from known value recorded in './previous_results/posterior_approx_logit_fixed_E.RDS'.
  Component "state_vecs": Mean relative difference: 0.09889156
  Component "state_vecs": Mean relative difference: 0.09889156
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted