Running ‘testthat.R’ [36s/59s]
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
  > # or maybe https://github.com/r-lib/devtools/issues/1526
  > Sys.unsetenv("R_TESTS")
  > 
  > options(deparse.max.lines = 5,  testthat.summary.max_reports = 1000L)
  > 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
  GMA: 
  Running tests for GMA: ..................
  LAPACK_BLAS: 
  Testing LAPACK wrapper functions: ..............................................
  PF: 
  Running test_PF: ........................................................................................................................................................................................................SS...SSSSSSSS..S..SS..SSSSSSSSSSSS
  SMA: 
  Testing SMA: ................S..............
  UKF: 
  Testing UKF: .........................
  bigglm_wrapper: 
  Testing bigglm_wrapper: ......SS
  boot_est: 
  Testing boot: ...S..................................................................................................................................................................................................................................................................................................................................................................................................................
  cloglog: 
  testing cloglog link function: ....S
  cpp_sample_funcs: 
  Testing cpp sampling functions: S..S.............................................................S....
  cpp_utils: 
  Running test_cpp_utils.R:: .S............
  ddhazard_n_EKF: 
  Testing ddhazard w/ generic things and w/ the the EKF: .....................S................
  design_mat_and_risk_obj: 
  Testing design_mat_and_risk_obj: ..................................................................................................................................................................................................................................................................................................................................................1...............................................2......................................................
  fixed_effects_in_E_step: 
  Testing fixed_effects_in_E_step: .........
  fixed_effects_in_M_step: 
  Testing test_fixed_effects_in_M_step: ..........S..
  get_start_values: 
  Testing 'get_start_values': ....................
  hatvalues: 
  Running tests for hatvalues: ....
  help_page_examples: 
  Testing examples in man files: .......S.S....SSSS........S
  loglike: 
  Testing loglike: ........................
  options: 
  Testing options: .
  parallelglm: 
  Testing parallelglm vs. glm: ................................................S
  plot: 
  Testing plot functions: ......................................
  predict: 
  Testing predict: ...............................................................................SS
  print: 
  Testing print function: ...SS.....
  residuals: 
  Testing residuals functions: ..................................................................................................................................................................................................SS
  shiny_app: 
  Testing shiny app: ..
  static_glm: 
  Testing static_glm: .............................
  summary: 
  Testing summary function: .................
  test_utils: 
  Testing test_utils: ............S......................................
  weights: 
  Testing weights in fit: ................
  
  ══ Skipped ═════════════════════════════════════════════════════════════════════
  1. PF_smooth gives same results (test_PF.R:71:3) - Reason: On CRAN
  
  2. Import and export PF cloud from Rcpp gives the same (test_PF.R:251:3) - Reason: On CRAN
  
  3. PF_EM gives previous results on head neck data set (test_PF.R:344:3) - Reason: On CRAN
  
  4. PF_EM gives previous results on head neck data set with fixed effects and the logit model (test_PF.R:411:3) - Reason: On CRAN
  
  5. compute_PF_summary_stats gives previous results (test_PF.R:436:3) - Reason: On CRAN
  
  6. 'get_cloud_means' and 'get_cloud_quantiles' gives previous results (test_PF.R:510:3) - Reason: On CRAN
  
  7. 'get_ancestors' yields the correct result (test_PF.R:560:3) - Reason: On CRAN
  
  8. ´est_params_dens´ gives the same as a R version (test_PF.R:582:3) - Reason: On CRAN
  
  9. fixed effect estimation gives the same as an R implementation (test_PF.R:630:3) - Reason: On CRAN
  
  10. A few iterations with `type = "VAR"' yields the same as before (test_PF.R:711:3) - Reason: On CRAN
  
  11. PF_EM gives the same with restricted and unrestricted model when we estimate all the parameters (test_PF.R:783:3) - Reason: On CRAN
  
  12. Using `n_smooth_final` works as expected and yields previous results (test_PF.R:896:3) - Reason: On CRAN
  
  13. sampling with a t-distribution gives previous results (test_PF.R:964:3) - Reason: On CRAN
  
  14. 'PF_forward_filter' gives the same as 'PF_EM' when it should (test_PF.R:1002:3) - Reason: On CRAN
  
  15. 'state_fw' gives correct results (test_PF.R:1131:3) - Reason: !dir.exists("pf-internals") is TRUE
  
  16. 'state_bw' gives correct results (test_PF.R:1167:3) - Reason: !dir.exists("pf-internals") is TRUE
  
  17. 'artificial_prior' gives correct results (test_PF.R:1202:3) - Reason: !dir.exists("pf-internals") is TRUE
  
  18. 'observational_cdist' gives correct results (test_PF.R:1236:3) - Reason: !dir.exists("pf-internals") is TRUE
  
  19. combining forward and backwards works (test_PF.R:1281:3) - Reason: !dir.exists("pf-internals") is TRUE
  
  20. combining prior and backwards works (test_PF.R:1328:3) - Reason: !dir.exists("pf-internals") is TRUE
  
  21. mode approximations give expected result (test_PF.R:1366:3) - Reason: !dir.exists("pf-internals") is TRUE
  
  22. 'PF_get_score_n_hess' gives the same as an R implementation (test_PF.R:1486:3) - Reason: On CRAN
  
  23. warns with randow walk model when covariates are in both fixed and random (test_PF.R:1624:3) - Reason: On CRAN
  
  24. works when there are time periods outside where we have data and with a single fixed and random effect (test_PF.R:1645:3) - Reason: On CRAN
  
  25. 'fix_seed = FALSE' yields different results at each call (test_PF.R:1670:3) - Reason: On CRAN
  
  26. Chaning the learning changes the result for the posterior approx method (test_SMA.R:120:3) - Reason: On CRAN
  
  27. bigglm and my c++ version yields similar results with offsets (test_bigglm_wrapper.R:298:5) - Reason: bigglm failed (likely biglm error in 0.9-1 release)
  
  28. bigglm and my c++ version yields similar with weights (test_bigglm_wrapper.R:328:5) - Reason: bigglm failed (likely biglm error in 0.9-1 release)
  
  29. boot yields previously computed values with pbc (test_boot_est.R:19:3) - Reason: On CRAN
  
  30. cloglog function gives previous result with simulated data using PF_EM and PF_forward_filter (test_cloglog.R:56:3) - Reason: On CRAN
  
  31. sample_indices give the same as R with same seed (test_cpp_sample_funcs.R:4:3) - Reason: On CRAN
  
  32. mvrnorm gives expected sample mean and variance (test_cpp_sample_funcs.R:51:3) - Reason: On CRAN
  
  33. 'mvtrnorm' yields close to uniform sample (test_cpp_sample_funcs.R:112:3) - Reason: On CRAN
  
  34. trunc_lp_in_exponential_dist does not truncate when not needed (test_cpp_utils.R:12:3) - Reason: On CRAN
  
  35. Different non-integer time_scales gives the same result with ddhazard (test_ddhazard_n_EKF.R:165:3) - Reason: On CRAN
  
  36. posterior_approx gives previous found values with fixed effects in M-step (test_fixed_effects_in_M_step.R:187:3) - Reason: On CRAN
  
  37. residuals.ddhazard help page examples gives the same results (test_help_page_examples.R:43:3) - Reason: On CRAN
  
  38. ddhazard_boot help page examples gives the same results (test_help_page_examples.R:67:3) - Reason: On CRAN
  
  39. PF_EM help page example runs and gives previous computed results (test_help_page_examples.R:129:3) - Reason: On CRAN
  
  40. Second example on PF help page gives the same result (test_help_page_examples.R:171:3) - Reason: On CRAN
  
  41. example in 'PF_EM' with gives previous results w/ a few iterations (test_help_page_examples.R:227:3) - Reason: On CRAN
  
  42. `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:358:3) - Reason: On CRAN
  
  43. 'PF_get_score_n_hess' gives previous results (test_help_page_examples.R:516:3) - Reason: On CRAN
  
  44. glm and parallelglm gives the same (test_parallelglm.R:80:3) - Reason: On CRAN
  
  45. Terms from predict with exponential outcome are correct (test_predict.R:413:3) - Reason: On CRAN
  
  46. Different non-integer time_scales gives the same result with predict results (test_predict.R:474:3) - Reason: On CRAN
  
  47. print.ddhazard_boot gives the expected output (test_print.R:39:3) - Reason: On CRAN
  
  48. Print function for PF objects gives previous results (test_print.R:89:3) - Reason: On CRAN
  
  49. Gets previous results with Rossi (test_residuals.R:209:3) - Reason: On CRAN
  
  50. Get prevoius residuals with whas500 (test_residuals.R:236:3) - Reason: On CRAN
  
  51. Testing util functions to sim series for tests (test_test_utils.R:28:3) - Reason: On CRAN
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Error (test_design_mat_and_risk_obj.R:583:3): Permutating gives the data f
  Error: cannot mtfrm
  Backtrace:
   1. testthat::expect_true(...) test_design_mat_and_risk_obj.R:583:2
   4. base::match(X_Y_org$Y, X_Y$Y)
   6. base::mtfrm.default(...)
  
  ── 2. Error (test_design_mat_and_risk_obj.R:644:3): Ordering gives the data fram
  Error: cannot mtfrm
  Backtrace:
   1. testthat::expect_true(...) test_design_mat_and_risk_obj.R:644:2
   4. base::match(X_Y_org$Y, X_Y$Y)
   6. base::mtfrm.default(...)
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted