CRAN Package Check Results for Package dynamichazard

Last updated on 2021-01-26 10:13:15 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.6.7	642.76	234.22	876.98	ERROR
r-devel-linux-x86_64-debian-gcc	0.6.7	441.44	173.30	614.74	ERROR
r-devel-linux-x86_64-fedora-clang	0.6.7			1197.47	ERROR
r-devel-linux-x86_64-fedora-gcc	0.6.7			1137.90	ERROR
r-devel-windows-ix86+x86_64	0.6.7	1460.00	412.00	1872.00	ERROR
r-patched-linux-x86_64	0.6.7	531.74	223.44	755.18	ERROR
r-patched-solaris-x86	0.6.7			969.90	ERROR
r-release-linux-x86_64	0.6.7	533.58	221.45	755.03	ERROR
r-release-macos-x86_64	0.6.7				NOTE
r-release-windows-ix86+x86_64	0.6.7	1454.00	324.00	1778.00	ERROR
r-oldrel-macos-x86_64	0.6.7				NOTE
r-oldrel-windows-ix86+x86_64	0.6.7	1116.00	414.00	1530.00	ERROR

Check Details

Version: 0.6.7
Check: tests
Result: ERROR
     Running 'testthat.R' [57s/70s]
    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
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.6.7
Check: tests
Result: ERROR
     Running ‘testthat.R’ [39s/63s]
    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. ´est_params_dens´ 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
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.6.7
Check: installed package size
Result: NOTE
     installed size is 37.4Mb
     sub-directories of 1Mb or more:
     data 4.2Mb
     doc 1.7Mb
     libs 31.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.6.7
Check: tests
Result: ERROR
     Running ‘testthat.R’ [64s/84s]
    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. ´est_params_dens´ 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
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.6.7
Check: tests
Result: ERROR
     Running ‘testthat.R’ [66s/86s]
    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. ´est_params_dens´ 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
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.6.7
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'testthat.R' [65s]
    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. ´est_params_dens´ 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
Flavor: r-devel-windows-ix86+x86_64

Version: 0.6.7
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'testthat.R' [67s]
    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. ´est_params_dens´ 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
Flavor: r-devel-windows-ix86+x86_64

Version: 0.6.7
Check: tests
Result: ERROR
     Running ‘testthat.R’ [55s/65s]
    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. ´est_params_dens´ 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
Flavor: r-patched-linux-x86_64

Version: 0.6.7
Check: tests
Result: ERROR
     Running ‘testthat.R’ [87s/108s]
    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..SSSS..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. ´est_params_dens´ 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. type = 'VAR' works with non-zero mean with a single term and gives previous results (test_PF.R:852:3) - Reason: On Solaris

     13. Using `n_smooth_final` works as expected and yields previous results (test_PF.R:894:3) - Reason: On CRAN

     14. sampling with a t-distribution gives previous results (test_PF.R:962:3) - Reason: On CRAN

     15. 'PF_forward_filter' gives the same as 'PF_EM' when it should (test_PF.R:1000:3) - Reason: On CRAN

     16. 'state_fw' gives correct results (test_PF.R:1129:3) - Reason: !dir.exists("pf-internals") is TRUE

     17. 'state_bw' gives correct results (test_PF.R:1165:3) - Reason: !dir.exists("pf-internals") is TRUE

     18. 'artificial_prior' gives correct results (test_PF.R:1200:3) - Reason: !dir.exists("pf-internals") is TRUE

     19. 'observational_cdist' gives correct results (test_PF.R:1234:3) - Reason: !dir.exists("pf-internals") is TRUE

     20. combining forward and backwards works (test_PF.R:1279:3) - Reason: !dir.exists("pf-internals") is TRUE

     21. combining prior and backwards works (test_PF.R:1326:3) - Reason: !dir.exists("pf-internals") is TRUE

     22. mode approximations give expected result (test_PF.R:1364:3) - Reason: !dir.exists("pf-internals") is TRUE

     23. 'PF_get_score_n_hess' gives the same as an R implementation (test_PF.R:1484:3) - Reason: On CRAN

     24. warns with randow walk model when covariates are in both fixed and random (test_PF.R:1622:3) - Reason: On CRAN

     25. 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

     26. 'fix_seed = FALSE' yields different results at each call (test_PF.R:1668:3) - Reason: On CRAN

     27. Chaning the learning changes the result for the posterior approx method (test_SMA.R:120:3) - Reason: On CRAN

     28. boot yields previously computed values with pbc (test_boot_est.R:19:3) - Reason: On CRAN

     29. cloglog function gives previous result with simulated data using PF_EM and PF_forward_filter (test_cloglog.R:56:3) - Reason: On CRAN

     30. mvrnorm gives expected sample mean and variance (test_cpp_sample_funcs.R:50:3) - Reason: On CRAN

     31. 'mvtrnorm' yields close to uniform sample (test_cpp_sample_funcs.R:111:3) - Reason: On CRAN

     32. trunc_lp_in_exponential_dist does not truncate when not needed (test_cpp_utils.R:12:3) - Reason: On CRAN

     33. Different non-integer time_scales gives the same result with ddhazard (test_ddhazard_n_EKF.R:165:3) - Reason: On CRAN

     34. posterior_approx gives previous found values with fixed effects in M-step (test_fixed_effects_in_M_step.R:187:3) - Reason: On CRAN

     35. residuals.ddhazard help page examples gives the same results (test_help_page_examples.R:43:3) - Reason: On CRAN

     36. ddhazard_boot help page examples gives the same results (test_help_page_examples.R:67:3) - Reason: On CRAN

     37. PF_EM help page example runs and gives previous computed results (test_help_page_examples.R:129:3) - Reason: On CRAN

     38. Second example on PF help page gives the same result (test_help_page_examples.R:170:3) - Reason: On CRAN

     39. example in 'PF_EM' with gives previous results w/ a few iterations (test_help_page_examples.R:226:3) - Reason: On CRAN

     40. `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

     41. 'PF_get_score_n_hess' gives previous results (test_help_page_examples.R:515:3) - Reason: On CRAN

     42. glm and parallelglm gives the same (test_parallelglm.R:80:3) - Reason: On CRAN

     43. Terms from predict with exponential outcome are correct (test_predict.R:413:3) - Reason: On CRAN

     44. Different non-integer time_scales gives the same result with predict results (test_predict.R:474:3) - Reason: On CRAN

     45. print.ddhazard_boot gives the expected output (test_print.R:39:3) - Reason: On CRAN

     46. Print function for PF objects gives previous results (test_print.R:89:3) - Reason: On CRAN

     47. Gets previous results with Rossi (test_residuals.R:209:3) - Reason: On CRAN

     48. Get prevoius residuals with whas500 (test_residuals.R:236:3) - Reason: On CRAN

     49. 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
Flavor: r-patched-solaris-x86

Version: 0.6.7
Check: tests
Result: ERROR
     Running ‘testthat.R’ [54s/63s]
    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. ´est_params_dens´ 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
Flavor: r-release-linux-x86_64

Version: 0.6.7
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'testthat.R' [53s]
    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. ´est_params_dens´ 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
Flavor: r-release-windows-ix86+x86_64

Version: 0.6.7
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'testthat.R' [52s]
    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. ´est_params_dens´ 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
Flavor: r-release-windows-ix86+x86_64

Version: 0.6.7
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'testthat.R' [68s]
    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. ´est_params_dens´ 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
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.6.7
Check: running tests for arch ‘x64’
Result: ERROR
     Running 'testthat.R' [69s]
    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. ´est_params_dens´ 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
Flavor: r-oldrel-windows-ix86+x86_64