Running ‘testthat.R’ [82s/82s]
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: ..................
  Testing LAPACK wrapper functions: ..........................................
  Running test_PF: ....................................................................................................SS...SSSSSS..S1
  Testing SMA: ................................
  Testing UKF: .........................
  Testing bigglm_wrapper: ..........
  Testing boot: ...S..................................................................................................................................................................................................................................................................................................................................................................................................................
  Testing cpp sampling functions: ..................................................................................................................................................................................................................................................................................................................................................................................................................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
  Testing loglike: ........................
  Testing options: .
  Testing parallelglm vs. glm: ................................S
  Testing plot functions: ......................................
  Testing predict: .............................................................S
  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#33) - On CRAN
  
  2. Import and export PF cloud from Rcpp gives the same (@test_PF.R#210) - On CRAN
  
  3. PF_EM gives previous results on head neck data set (@test_PF.R#272) - On CRAN
  
  4. PF_EM gives previous results on head neck data set with fixed effects and the logit model (@test_PF.R#339) - On CRAN
  
  5. compute_PF_summary_stats gives previous results (@test_PF.R#362) - On CRAN
  
  6. ´est_params_dens´ gives the same as a R version (@test_PF.R#436) - On CRAN
  
  7. fixed effect estimation gives the same as an R implementation (@test_PF.R#484) - On CRAN
  
  8. A few iterations with `type = "VAR"' yields the same as before (@test_PF.R#565) - On CRAN
  
  9. PF_EM gives the same with restricted and unrestricted model when we estimate all the parameters (@test_PF.R#646) - On CRAN
  
  10. boot yields previously computed values with pbc (@test_boot_est.R#19) - On CRAN
  
  11. mvrnorm gives expected sample mean and variance (@test_cpp_sample_funcs.R#50) - On CRAN
  
  12. trunc_lp_in_exponential_dist does not truncate when not needed (@test_cpp_utils.R#12) - On CRAN
  
  13. Different non-integer time_scales gives the same result with ddhazard (@test_ddhazard_n_EKF.R#165) - On CRAN
  
  14. posterior_approx gives previous found values with fixed effects in M-step (@test_fixed_effects_in_M_step.R#187) - On CRAN
  
  15. residuals.ddhazard help page examples gives the same results (@test_help_page_examples.R#43) - On CRAN
  
  16. ddhazard_boot help page examples gives the same results (@test_help_page_examples.R#67) - On CRAN
  
  17. PF_EM help page example runs and gives previous computed results (@test_help_page_examples.R#130) - On CRAN
  
  18. Second example on PF help page gives the same result (@test_help_page_examples.R#169) - On CRAN
  
  19. example in 'PF_EM' with gives previous results w/ a few iterations (@test_help_page_examples.R#223) - On CRAN
  
  20. `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#352) - On CRAN
  
  21. glm and parallelglm gives the same (@test_parallelglm.R#64) - On CRAN
  
  22. Different non-integer time_scales gives the same result with predict results (@test_predict.R#366) - On CRAN
  
  23. print.ddhazard_boot gives the expected output (@test_print.R#39) - On CRAN
  
  24. Print function for PF objects gives previous results (@test_print.R#89) - On CRAN
  
  25. Gets previous results with Rossi (@test_residuals.R#209) - On CRAN
  
  26. Get prevoius residuals with whas500 (@test_residuals.R#236) - On CRAN
  
  27. Testing util functions to sim series for tests (@test_test_utils.R#28) - On CRAN
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Error: type = 'VAR' works with non-zero mean for with a single term and gi
  BLAS/LAPACK routine 'DTRTRS' gave error code -7
  1: suppressWarnings(PF_EM(Surv(start, stop, event) ~ ddFixed(group) + ddFixed_intercept(TRUE), 
         head_neck_cancer, Q_0 = 1, Q = 0.2, Fmat = diag(0.01, 1), by = 1, type = "VAR", 
         model = "logit", max_T = 30, control = PF_control(N_fw_n_bw = 50, N_smooth = 100, 
             N_first = 500, eps = 0.001, method = "AUX_normal_approx_w_cloud_mean", n_max = 2, 
             smoother = "Fearnhead_O_N", Q_tilde = diag(0.3^2, 1), n_threads = 1))) at testthat/test_PF.R:733
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: PF_EM(Surv(start, stop, event) ~ ddFixed(group) + ddFixed_intercept(TRUE), head_neck_cancer, 
         Q_0 = 1, Q = 0.2, Fmat = diag(0.01, 1), by = 1, type = "VAR", model = "logit", 
         max_T = 30, control = PF_control(N_fw_n_bw = 50, N_smooth = 100, N_first = 500, 
             eps = 0.001, method = "AUX_normal_approx_w_cloud_mean", n_max = 2, smoother = "Fearnhead_O_N", 
             Q_tilde = diag(0.3^2, 1), n_threads = 1))
  4: .PF_EM(trace = trace, seed = seed, fixed_parems = fixed_parems, type = type, n_fixed_terms_in_state_vec = static_args$n_fixed_terms_in_state_vec, 
         X = static_args$X, fixed_terms = static_args$fixed_terms, tstart = static_args$tstart, 
         tstop = static_args$tstop, risk_obj = static_args$risk_obj, debug = static_args$debug, 
         model = static_args$model, Q = model_args$Q, Q_0 = model_args$Q_0, F. = model_args$F., 
         R = model_args$R, a_0 = model_args$a_0, G = model_args$G, J = model_args$J, K = model_args$K, 
  5: eval(fit_call, envir = parent.frame())
  6: eval(fit_call, envir = parent.frame())
  7: PF_smooth(n_fixed_terms_in_state_vec = static_args$n_fixed_terms_in_state_vec, X = static_args$X, 
         fixed_terms = static_args$fixed_terms, tstart = static_args$tstart, tstop = static_args$tstop, 
         Q_0 = structure(0.2000200020002, .Dim = c(1L, 1L)), Q = structure(0.2, .Dim = c(1L, 
         1L)), a_0 = 0, R = model_args$R, risk_obj = static_args$risk_obj, n_max = control$n_max, 
         n_threads = control$n_threads, N_fw_n_bw = control$N_fw_n_bw, N_smooth = control$N_smooth, 
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted