Running 'testthat.R' [56s/71s]
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.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: ..........
  boot_est: 
  Testing boot: ...S..................................................................................................................................................................................................................................................................................................................................................................................................................
  cloglog: 
  testing cloglog link function: ....S
  cpp_sample_funcs: 
  Testing cpp sampling functions: ..................................................................................................................................................................................................................................................................................................................................................................................................................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: ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
  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: ............1.......
  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:249:3) - Reason: On CRAN
  
  3. PF_EM gives previous results on head neck data set (test_PF.R:342:3) - Reason: On CRAN
  
  4. PF_EM gives previous results on head neck data set with fixed effects and the logit model (test_PF.R:409:3) - Reason: On CRAN
  
  5. compute_PF_summary_stats gives previous results (test_PF.R:434:3) - Reason: On CRAN
  
  6. 'get_cloud_means' and 'get_cloud_quantiles' gives previous results (test_PF.R:508:3) - Reason: On CRAN
  
  7. 'get_ancestors' yields the correct result (test_PF.R:558:3) - Reason: On CRAN
  
  8. <U+00B4>est_params_dens<U+00B4> gives the same as a R version (test_PF.R:580:3) - Reason: On CRAN
  
  9. fixed effect estimation gives the same as an R implementation (test_PF.R:628:3) - Reason: On CRAN
  
  10. A few iterations with `type = "VAR"' yields the same as before (test_PF.R:709:3) - Reason: On CRAN
  
  11. PF_EM gives the same with restricted and unrestricted model when we estimate all the parameters (test_PF.R:781:3) - Reason: On CRAN
  
  12. Using `n_smooth_final` works as expected and yields previous results (test_PF.R:894:3) - Reason: On CRAN
  
  13. sampling with a t-distribution gives previous results (test_PF.R:962:3) - Reason: On CRAN
  
  14. 'PF_forward_filter' gives the same as 'PF_EM' when it should (test_PF.R:1000:3) - Reason: On CRAN
  
  15. 'state_fw' gives correct results (test_PF.R:1129:3) - Reason: !dir.exists("pf-internals") is TRUE
  
  16. 'state_bw' gives correct results (test_PF.R:1165:3) - Reason: !dir.exists("pf-internals") is TRUE
  
  17. 'artificial_prior' gives correct results (test_PF.R:1200:3) - Reason: !dir.exists("pf-internals") is TRUE
  
  18. 'observational_cdist' gives correct results (test_PF.R:1234:3) - Reason: !dir.exists("pf-internals") is TRUE
  
  19. combining forward and backwards works (test_PF.R:1279:3) - Reason: !dir.exists("pf-internals") is TRUE
  
  20. combining prior and backwards works (test_PF.R:1326:3) - Reason: !dir.exists("pf-internals") is TRUE
  
  21. mode approximations give expected result (test_PF.R:1364:3) - Reason: !dir.exists("pf-internals") is TRUE
  
  22. 'PF_get_score_n_hess' gives the same as an R implementation (test_PF.R:1484:3) - Reason: On CRAN
  
  23. warns with randow walk model when covariates are in both fixed and random (test_PF.R:1622:3) - 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:1643:3) - Reason: On CRAN
  
  25. 'fix_seed = FALSE' yields different results at each call (test_PF.R:1668:3) - Reason: On CRAN
  
  26. Chaning the learning changes the result for the posterior approx method (test_SMA.R:120:3) - Reason: On CRAN
  
  27. boot yields previously computed values with pbc (test_boot_est.R:19:3) - Reason: On CRAN
  
  28. cloglog function gives previous result with simulated data using PF_EM and PF_forward_filter (test_cloglog.R:56:3) - Reason: On CRAN
  
  29. mvrnorm gives expected sample mean and variance (test_cpp_sample_funcs.R:50:3) - Reason: On CRAN
  
  30. 'mvtrnorm' yields close to uniform sample (test_cpp_sample_funcs.R:111:3) - Reason: On CRAN
  
  31. trunc_lp_in_exponential_dist does not truncate when not needed (test_cpp_utils.R:12:3) - Reason: On CRAN
  
  32. Different non-integer time_scales gives the same result with ddhazard (test_ddhazard_n_EKF.R:165:3) - Reason: On CRAN
  
  33. posterior_approx gives previous found values with fixed effects in M-step (test_fixed_effects_in_M_step.R:187:3) - Reason: On CRAN
  
  34. residuals.ddhazard help page examples gives the same results (test_help_page_examples.R:43:3) - Reason: On CRAN
  
  35. ddhazard_boot help page examples gives the same results (test_help_page_examples.R:67:3) - Reason: On CRAN
  
  36. PF_EM help page example runs and gives previous computed results (test_help_page_examples.R:129:3) - Reason: On CRAN
  
  37. Second example on PF help page gives the same result (test_help_page_examples.R:170:3) - Reason: On CRAN
  
  38. example in 'PF_EM' with gives previous results w/ a few iterations (test_help_page_examples.R:226:3) - Reason: On CRAN
  
  39. `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:357:3) - Reason: On CRAN
  
  40. 'PF_get_score_n_hess' gives previous results (test_help_page_examples.R:515:3) - Reason: On CRAN
  
  41. glm and parallelglm gives the same (test_parallelglm.R:80:3) - Reason: On CRAN
  
  42. Terms from predict with exponential outcome are correct (test_predict.R:413:3) - Reason: On CRAN
  
  43. Different non-integer time_scales gives the same result with predict results (test_predict.R:474:3) - Reason: On CRAN
  
  44. print.ddhazard_boot gives the expected output (test_print.R:39:3) - Reason: On CRAN
  
  45. Print function for PF objects gives previous results (test_print.R:89:3) - Reason: On CRAN
  
  46. Gets previous results with Rossi (test_residuals.R:209:3) - Reason: On CRAN
  
  47. Get prevoius residuals with whas500 (test_residuals.R:236:3) - Reason: On CRAN
  
  48. Testing util functions to sim series for tests (test_test_utils.R:28:3) - Reason: On CRAN
  
  == Failed ======================================================================
  -- 1. Error (test_static_glm.R:130:5): Gets same with different methods --------
  Error: object 'c_weights' not found
  Backtrace:
    1. dynamichazard:::get_fit("speedglm") test_static_glm.R:130:4
    2. dynamichazard::static_glm(...) test_static_glm.R:124:15
    5. dynamichazard:::.static_glm_fit(...)
   10. stats::model.frame.default(...)
   11. [ base::eval(...) ] with 1 more call
  
  == DONE ========================================================================
  Error: Test failures
  Execution halted