CRAN Package Check Results for Package dynamichazard

Last updated on 2019-11-22 03:49:13 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.6.6 OK
r-devel-linux-x86_64-debian-gcc 0.6.6 445.30 161.06 606.36 OK
r-devel-linux-x86_64-fedora-clang 0.6.6 1154.04 NOTE
r-devel-linux-x86_64-fedora-gcc 0.6.6 1056.13 OK
r-devel-windows-ix86+x86_64 0.6.6 1399.00 415.00 1814.00 NOTE
r-devel-windows-ix86+x86_64-gcc8 0.6.6 1240.00 319.00 1559.00 NOTE
r-patched-linux-x86_64 0.6.6 463.78 195.75 659.53 OK
r-patched-solaris-x86 0.6.6 943.50 ERROR
r-release-linux-x86_64 0.6.6 477.23 195.43 672.66 OK
r-release-windows-ix86+x86_64 0.6.6 1351.00 318.00 1669.00 NOTE
r-release-osx-x86_64 0.6.6 NOTE
r-oldrel-windows-ix86+x86_64 0.6.6 1028.00 417.00 1445.00 NOTE
r-oldrel-osx-x86_64 0.6.6 NOTE

Additional issues

LTO

Check Details

Version: 0.6.6
Check: installed package size
Result: NOTE
     installed size is 35.4Mb
     sub-directories of 1Mb or more:
     data 4.2Mb
     doc 1.7Mb
     libs 29.0Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.6.6
Check: tests
Result: ERROR
     Running ‘testthat.R’ [99s/119s]
    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
     Running tests for GMA: ..................
     Testing LAPACK wrapper functions: ..............................................
     Running test_PF: ........................................................................................................................................................................................................SS...SSSSSSSS..S12SS..SSSSSSSSSSSS
     Testing SMA: ................................
     Testing UKF: .........................
     Testing bigglm_wrapper: ..........
     Testing boot: ...S..................................................................................................................................................................................................................................................................................................................................................................................................................
     testing cloglog link function: ....S
     Testing cpp sampling functions: ..................................................................................................................................................................................................................................................................................................................................................................................................................S.............................................................S....
     Running test_cpp_utils.R:: .S............
     Testing ddhazard w/ generic things and w/ the the EKF : .....................S................
     Testing design_mat_and_risk_obj: ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
     Testing fixed_effects_in_E_step: .........
     Testing test_fixed_effects_in_M_step: ..........S..
     Testing 'get_start_values': ....................
     Running tests for hatvalues: ....
     Testing examples in man files: .......S.S....SSSS........S
     Testing loglike: ........................
     Testing options: .
     Testing parallelglm vs. glm: ................................................S
     Testing plot functions: ......................................
     Testing predict: ...............................................................................SS
     Testing print function: ...SS.....
     Testing residuals functions: ..................................................................................................................................................................................................SS
     Testing shiny app: ..
     Testing static_glm: .............................
     Testing summary function: .................
     Testing test_utils: ............S......................................
     Testing weights in fit: ................
    
     ══ Skipped ═════════════════════════════════════════════════════════════════════
     1. PF_smooth gives same results (@test_PF.R#71) - Reason: On CRAN
    
     2. Import and export PF cloud from Rcpp gives the same (@test_PF.R#249) - Reason: On CRAN
    
     3. PF_EM gives previous results on head neck data set (@test_PF.R#342) - 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) - Reason: On CRAN
    
     5. compute_PF_summary_stats gives previous results (@test_PF.R#434) - Reason: On CRAN
    
     6. 'get_cloud_means' and 'get_cloud_quantiles' gives previous results (@test_PF.R#508) - Reason: On CRAN
    
     7. 'get_ancestors' yields the correct result (@test_PF.R#558) - Reason: On CRAN
    
     8. ´est_params_dens´ gives the same as a R version (@test_PF.R#580) - Reason: On CRAN
    
     9. fixed effect estimation gives the same as an R implementation (@test_PF.R#628) - Reason: On CRAN
    
     10. A few iterations with `type = "VAR"' yields the same as before (@test_PF.R#709) - Reason: On CRAN
    
     11. PF_EM gives the same with restricted and unrestricted model when we estimate all the parameters (@test_PF.R#781) - Reason: On CRAN
    
     12. Using `n_smooth_final` works as expected and yields previous results (@test_PF.R#891) - Reason: On CRAN
    
     13. sampling with a t-distribution gives previous results (@test_PF.R#959) - Reason: On CRAN
    
     14. 'PF_forward_filter' gives the same as 'PF_EM' when it should (@test_PF.R#997) - Reason: On CRAN
    
     15. 'state_fw' gives correct results (@test_PF.R#1126) - Reason: !dir.exists("pf-internals") is TRUE
    
     16. 'state_bw' gives correct results (@test_PF.R#1162) - Reason: !dir.exists("pf-internals") is TRUE
    
     17. 'artificial_prior' gives correct results (@test_PF.R#1197) - Reason: !dir.exists("pf-internals") is TRUE
    
     18. 'observational_cdist' gives correct results (@test_PF.R#1231) - Reason: !dir.exists("pf-internals") is TRUE
    
     19. combining forward and backwards works (@test_PF.R#1276) - Reason: !dir.exists("pf-internals") is TRUE
    
     20. combining prior and backwards works (@test_PF.R#1323) - Reason: !dir.exists("pf-internals") is TRUE
    
     21. mode approximations give expected result (@test_PF.R#1361) - Reason: !dir.exists("pf-internals") is TRUE
    
     22. 'PF_get_score_n_hess' gives the same as an R implementation (@test_PF.R#1481) - Reason: On CRAN
    
     23. warns with randow walk model when covariates are in both fixed and random (@test_PF.R#1619) - 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#1640) - Reason: On CRAN
    
     25. 'fix_seed = FALSE' yields different results at each call (@test_PF.R#1665) - Reason: On CRAN
    
     26. boot yields previously computed values with pbc (@test_boot_est.R#19) - Reason: On CRAN
    
     27. cloglog function gives previous result with simulated data using PF_EM and PF_forward_filter (@test_cloglog.R#56) - Reason: On CRAN
    
     28. mvrnorm gives expected sample mean and variance (@test_cpp_sample_funcs.R#50) - Reason: On CRAN
    
     29. 'mvtrnorm' yields close to uniform sample (@test_cpp_sample_funcs.R#111) - Reason: On CRAN
    
     30. trunc_lp_in_exponential_dist does not truncate when not needed (@test_cpp_utils.R#12) - Reason: On CRAN
    
     31. Different non-integer time_scales gives the same result with ddhazard (@test_ddhazard_n_EKF.R#165) - Reason: On CRAN
    
     32. posterior_approx gives previous found values with fixed effects in M-step (@test_fixed_effects_in_M_step.R#187) - Reason: On CRAN
    
     33. residuals.ddhazard help page examples gives the same results (@test_help_page_examples.R#43) - Reason: On CRAN
    
     34. ddhazard_boot help page examples gives the same results (@test_help_page_examples.R#67) - Reason: On CRAN
    
     35. PF_EM help page example runs and gives previous computed results (@test_help_page_examples.R#129) - Reason: On CRAN
    
     36. Second example on PF help page gives the same result (@test_help_page_examples.R#170) - Reason: On CRAN
    
     37. example in 'PF_EM' with gives previous results w/ a few iterations (@test_help_page_examples.R#226) - Reason: On CRAN
    
     38. `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) - Reason: On CRAN
    
     39. 'PF_get_score_n_hess' gives previous results (@test_help_page_examples.R#515) - Reason: On CRAN
    
     40. glm and parallelglm gives the same (@test_parallelglm.R#80) - Reason: On CRAN
    
     41. Terms from predict with exponential outcome are correct (@test_predict.R#413) - Reason: On CRAN
    
     42. Different non-integer time_scales gives the same result with predict results (@test_predict.R#474) - Reason: On CRAN
    
     43. print.ddhazard_boot gives the expected output (@test_print.R#39) - Reason: On CRAN
    
     44. Print function for PF objects gives previous results (@test_print.R#89) - Reason: On CRAN
    
     45. Gets previous results with Rossi (@test_residuals.R#209) - Reason: On CRAN
    
     46. Get prevoius residuals with whas500 (@test_residuals.R#236) - Reason: On CRAN
    
     47. Testing util functions to sim series for tests (@test_test_utils.R#28) - Reason: On CRAN
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Failure: type = 'VAR' works with non-zero mean with a single term and give
     pf_Fear[!names(pf_Fear) %in% c("clouds", "terms")] has changed from known value recorded in './previous_results/PF_VARS_non_zero_mean_inter.RDS'.
     Component "fixed_effects": Mean relative difference: 0.003429579
     Component "Q": Mean relative difference: 0.007446987
     Component "F": Mean relative difference: 0.04211867
     Component "EM_ests": Component "fixed_effects": Mean relative difference: 0.001772855
     Component "EM_ests": Component "F": Mean relative difference: 0.03132344
     Component "EM_ests": Component "Q": Mean relative difference: 0.004506336
     Component "log_likes": Mean relative difference: 1.356319e-05
     Component "effective_sample_size": Component "forward_clouds": Mean relative difference: 0.01892254
     Component "effective_sample_size": Component "backward_clouds": Mean relative difference: 0.07728725
     ...
    
     ── 2. Failure: type = 'VAR' works with non-zero mean with a single term and give
     pf_Fear[!names(pf_Fear) %in% c("clouds", "terms")] has changed from known value recorded in './previous_results/PF_VARS_non_zero_mean_slope.RDS'.
     Component "Q": Mean relative difference: 0.01722249
     Component "F": Mean relative difference: 0.78695
     Component "EM_ests": Component "fixed_effects": Mean relative difference: 0.001158271
     Component "EM_ests": Component "F": Mean relative difference: 0.7408576
     Component "EM_ests": Component "Q": Mean relative difference: 0.01218133
     Component "effective_sample_size": Component "forward_clouds": Mean relative difference: 0.143008
     Component "effective_sample_size": Component "backward_clouds": Mean relative difference: 0.06038568
     Component "effective_sample_size": Component "smoothed_clouds": Mean relative difference: 0.01708075
     Component "seed": Mean relative difference: 0.007246377
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     Execution halted
Flavor: r-patched-solaris-x86