- using R version 3.6.3 (2020-02-29)
- using platform: x86_64-w64-mingw32 (64-bit)
- using session charset: ISO8859-1
- checking for file 'dynamichazard/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'dynamichazard' version '0.6.7'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'dynamichazard' can be installed ... OK
- checking installed package size ... NOTE
installed size is 11.4Mb
sub-directories of 1Mb or more:
data 4.2Mb
doc 1.7Mb
libs 5.1Mb
- checking package directory ... OK
- checking 'build' directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- loading checks for arch 'i386'
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking use of S3 registration ... OK
- loading checks for arch 'x64'
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [12s] OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of 'data' directory ... OK
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compiled code ... OK
- checking sizes of PDF files under 'inst/doc' ... OK
- checking installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ...
- running examples for arch 'i386' ... [8s] OK
- running examples for arch 'x64' ... [8s] OK
- checking for unstated dependencies in 'tests' ... OK
- checking tests ...
- running tests for arch 'i386' ... [57s] ERROR
Running 'testthat.R' [56s]
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
- running tests for arch 'x64' ... [59s] ERROR
Running 'testthat.R' [58s]
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
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in 'inst/doc' ... OK
- checking re-building of vignette outputs ... [79s] OK
- checking PDF version of manual ... OK
- DONE
Status: 2 ERRORs, 1 NOTE