CRAN Package Check Results for Package dynamichazard

Last updated on 2018-05-24 12:47:30 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.5.1 274.03 191.43 465.46 WARN
r-devel-linux-x86_64-debian-gcc 0.5.1 221.96 165.74 387.70 WARN
r-devel-linux-x86_64-fedora-clang 0.5.1 680.70 NOTE
r-devel-linux-x86_64-fedora-gcc 0.5.1 649.40 NOTE
r-devel-windows-ix86+x86_64 0.5.1 554.00 343.00 897.00 NOTE
r-patched-linux-x86_64 0.5.1 268.72 191.24 459.96 ERROR
r-patched-solaris-x86 0.5.1 618.60 NOTE
r-release-linux-x86_64 0.5.1 281.31 191.98 473.29 ERROR
r-release-windows-ix86+x86_64 0.5.1 711.00 398.00 1109.00 NOTE
r-release-osx-x86_64 0.5.1 NOTE
r-oldrel-windows-ix86+x86_64 0.5.1 685.00 416.00 1101.00 NOTE
r-oldrel-osx-x86_64 0.5.1 NOTE

Check Details

Version: 0.5.1
Check: for unstated dependencies in ‘tests’
Result: WARN
    '::' or ':::' imports not declared from:
     ‘gsl’ ‘mvtnorm’
    'library' or 'require' call not declared from: ‘plyr’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.5.1
Check: installed package size
Result: NOTE
     installed size is 22.7Mb
     sub-directories of 1Mb or more:
     data 4.2Mb
     doc 1.2Mb
     libs 16.9Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, 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: 0.5.1
Check: DESCRIPTION meta-information
Result: NOTE
    Dependence on R version ‘3.3.2’ not with patchlevel 0
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.5.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [52s/88s]
    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" = "")
     >
     > 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: SSS......SS
     Testing SMA: .................................
     Testing UKF: .........................
     Testing bigglm_wrapper: ....123
     Testing boot: ...S..................................................................................................................................................................................................................................................................................................................................................................................................................
     Testing cpp sampling functions: ..................................................................................................................................................................................................................................................................................................................................................................................................................S.............................................................
     Running test_cpp_utils.R:: SS...
     Testing ddhazard w/ generic things and w/ the the EKF : ..............S..............
     Testing design_mat_and_risk_obj: ................................................................S.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
     Testing fixed_effects_in_E_step: .........
     Testing test_fixed_effects_in_M_step: 4.5......S6
     Running tests for hatvalues: ....
     Testing loglike: ........................
     Testing options: .
     Testing parallelglm vs. glm: ................................S
     Testing plot functions: ......................................
     Testing predict: .............................................................S
     Testing print function: ...SS....
     Testing residuals functions: ..................................................................................................................................................................................................SS
     Testing shiny app: ..
     Testing static_glm: ....................
     Testing summary function: .................
     Testing test_utils: ............S......
     Testing weights in fit: ................
    
     ══ Skipped ═════════════════════════════════════════════════════════════════════
     1. dmvnrm_log_test gives correct likelihood (@test_PF.R#4) - mvtnorm cannot be loaded
    
     2. PF_smooth gives same results (@test_PF.R#35) - On CRAN
    
     3. Import and export PF cloud from Rcpp gives the same (@test_PF.R#222) - On CRAN
    
     4. PF_EM gives previous results on head neck data set (@test_PF.R#300) - On CRAN
    
     5. compute_summary_stats gives previous results (@test_PF.R#357) - On CRAN
    
     6. boot yields previously computed values with pbc (@test_boot_est.R#19) - On CRAN
    
     7. mvrnorm gives expected sample mean and variance (@test_cpp_sample_funcs.R#54) - On CRAN
    
     8. lambert_W0 gives close to same results as gsl::lambert_W0 (@test_cpp_utils.R#4) - gsl cannot be loaded
    
     9. trunc_lp_in_exponential_dist does not truncate when not needed (@test_cpp_utils.R#12) - On CRAN
    
     10. Different non-integer time_scales gives the same result with ddhazard (@test_ddhazard_n_EKF.R#136) - On CRAN
    
     11. Different forms of fixing the intercept gives same results (@test_design_mat_and_risk_obj.R#111) - On CRAN
    
     12. posterior_approx gives previous found values with fixed effects in M-step (@test_fixed_effects_in_M_step.R#168) - On CRAN
    
     13. glm and parallelglm gives the same (@test_parallelglm.R#61) - On CRAN
    
     14. Different non-integer time_scales gives the same result with predict results (@test_predict.R#367) - On CRAN
    
     15. print.ddhazard_boot gives the expected output (@test_print.R#39) - On CRAN
    
     16. Print function for PF objects gives previous results (@test_print.R#87) - On CRAN
    
     17. Gets previous results with Rossi (@test_residuals.R#210) - On CRAN
    
     18. Get prevoius residuals with whas500 (@test_residuals.R#236) - On CRAN
    
     19. Testing util functions to sim series for tests (@test_test_utils.R#28) - On CRAN
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Error: bigglm and my c++ version yields similar results (@test_bigglm_wrap
     no applicable method for 'bigglm' applied to an object of class "function"
     1: suppressWarnings(bigglm_res <- biglm::bigglm(form, get_data_func, family = if (model ==
     "logit") binomial() else poisson())) at testthat/test_bigglm_wrapper.R:266
     2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     3: biglm::bigglm(form, get_data_func, family = if (model == "logit") binomial() else poisson())
     4: biglm::bigglm(form, get_data_func, family = if (model == "logit") binomial() else poisson())
    
     ── 2. Error: bigglm and my c++ version yields similar results with offsets (@tes
     no applicable method for 'bigglm' applied to an object of class "function"
     1: suppressWarnings(bigglm_res <- biglm::bigglm(form, get_data_func, family = if (model ==
     "logit") binomial() else poisson())) at testthat/test_bigglm_wrapper.R:285
     2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     3: biglm::bigglm(form, get_data_func, family = if (model == "logit") binomial() else poisson())
     4: biglm::bigglm(form, get_data_func, family = if (model == "logit") binomial() else poisson())
    
     ── 3. Error: bigglm and my c++ version yields similar with weights (@test_bigglm
     no applicable method for 'bigglm' applied to an object of class "function"
     1: suppressWarnings(bigglm_res <- biglm::bigglm(form, get_data_func, family = if (model ==
     "logit") binomial() else poisson(), weights = ~ws)) at testthat/test_bigglm_wrapper.R:308
     2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     3: biglm::bigglm(form, get_data_func, family = if (model == "logit") binomial() else poisson(),
     weights = ~ws)
     4: biglm::bigglm(form, get_data_func, family = if (model == "logit") binomial() else poisson(),
     weights = ~ws)
    
     ── 4. Error: Only fixed effects yields same results as bigglm with logit model (
     no applicable method for 'bigglm' applied to an object of class "data.frame"
     1: suppressWarnings(res2 <- bigglm(update(form, Y ~ . - ddFixed_intercept()), data = tmp_design$X,
     family = binomial(), chunksize = 1000)) at testthat/test_fixed_effects_in_M_step.R:24
     2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     3: bigglm(update(form, Y ~ . - ddFixed_intercept()), data = tmp_design$X, family = binomial(),
     chunksize = 1000)
     4: bigglm(update(form, Y ~ . - ddFixed_intercept()), data = tmp_design$X, family = binomial(),
     chunksize = 1000)
    
     ── 5. Error: Only fixed effects yields same results as bigglm with exponential m
     no applicable method for 'bigglm' applied to an object of class "data.frame"
     1: suppressWarnings(res2 <- bigglm(update(form, Y ~ . - ddFixed_intercept() + offset(log(pmin(tstop,
     t) - pmax(tstart, t - 1)))), data = tmp_design$X, family = poisson(), chunksize = 1000,
     tolerance = 1e-04)) at testthat/test_fixed_effects_in_M_step.R:65
     2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     3: bigglm(update(form, Y ~ . - ddFixed_intercept() + offset(log(pmin(tstop, t) - pmax(tstart,
     t - 1)))), data = tmp_design$X, family = poisson(), chunksize = 1000, tolerance = 1e-04)
     4: bigglm(update(form, Y ~ . - ddFixed_intercept() + offset(log(pmin(tstop, t) - pmax(tstart,
     t - 1)))), data = tmp_design$X, family = poisson(), chunksize = 1000, tolerance = 1e-04)
    
     ── 6. Error: Only fixed effects yields same results as bigglm with exponential m
     no applicable method for 'bigglm' applied to an object of class "data.frame"
     1: suppressWarnings(res2 <- bigglm(update(form, Y ~ . - ddFixed_intercept() + offset(log(pmin(tstop,
     t) - pmax(tstart, t - 1)))), data = tmp_design$X, family = poisson(), chunksize = 1000,
     tolerance = 1e-04, weights = ~ws)) at testthat/test_fixed_effects_in_M_step.R:207
     2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     3: bigglm(update(form, Y ~ . - ddFixed_intercept() + offset(log(pmin(tstop, t) - pmax(tstart,
     t - 1)))), data = tmp_design$X, family = poisson(), chunksize = 1000, tolerance = 1e-04,
     weights = ~ws)
     4: bigglm(update(form, Y ~ . - ddFixed_intercept() + offset(log(pmin(tstop, t) - pmax(tstart,
     t - 1)))), data = tmp_design$X, family = poisson(), chunksize = 1000, tolerance = 1e-04,
     weights = ~ws)
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 0.5.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [53s/94s]
    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" = "")
     >
     > 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: SSS......SS
     Testing SMA: .................................
     Testing UKF: .........................
     Testing bigglm_wrapper: ....123
     Testing boot: ...S..................................................................................................................................................................................................................................................................................................................................................................................................................
     Testing cpp sampling functions: ..................................................................................................................................................................................................................................................................................................................................................................................................................S.............................................................
     Running test_cpp_utils.R:: SS...
     Testing ddhazard w/ generic things and w/ the the EKF : ..............S..............
     Testing design_mat_and_risk_obj: ................................................................S.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
     Testing fixed_effects_in_E_step: .........
     Testing test_fixed_effects_in_M_step: 4.5......S6
     Running tests for hatvalues: ....
     Testing loglike: ........................
     Testing options: .
     Testing parallelglm vs. glm: ................................S
     Testing plot functions: ......................................
     Testing predict: .............................................................S
     Testing print function: ...SS....
     Testing residuals functions: ..................................................................................................................................................................................................SS
     Testing shiny app: ..
     Testing static_glm: ....................
     Testing summary function: .................
     Testing test_utils: ............S......
     Testing weights in fit: ................
    
     ══ Skipped ═════════════════════════════════════════════════════════════════════
     1. dmvnrm_log_test gives correct likelihood (@test_PF.R#4) - mvtnorm cannot be loaded
    
     2. PF_smooth gives same results (@test_PF.R#35) - On CRAN
    
     3. Import and export PF cloud from Rcpp gives the same (@test_PF.R#222) - On CRAN
    
     4. PF_EM gives previous results on head neck data set (@test_PF.R#300) - On CRAN
    
     5. compute_summary_stats gives previous results (@test_PF.R#357) - On CRAN
    
     6. boot yields previously computed values with pbc (@test_boot_est.R#19) - On CRAN
    
     7. mvrnorm gives expected sample mean and variance (@test_cpp_sample_funcs.R#54) - On CRAN
    
     8. lambert_W0 gives close to same results as gsl::lambert_W0 (@test_cpp_utils.R#4) - gsl cannot be loaded
    
     9. trunc_lp_in_exponential_dist does not truncate when not needed (@test_cpp_utils.R#12) - On CRAN
    
     10. Different non-integer time_scales gives the same result with ddhazard (@test_ddhazard_n_EKF.R#136) - On CRAN
    
     11. Different forms of fixing the intercept gives same results (@test_design_mat_and_risk_obj.R#111) - On CRAN
    
     12. posterior_approx gives previous found values with fixed effects in M-step (@test_fixed_effects_in_M_step.R#168) - On CRAN
    
     13. glm and parallelglm gives the same (@test_parallelglm.R#61) - On CRAN
    
     14. Different non-integer time_scales gives the same result with predict results (@test_predict.R#367) - On CRAN
    
     15. print.ddhazard_boot gives the expected output (@test_print.R#39) - On CRAN
    
     16. Print function for PF objects gives previous results (@test_print.R#87) - On CRAN
    
     17. Gets previous results with Rossi (@test_residuals.R#210) - On CRAN
    
     18. Get prevoius residuals with whas500 (@test_residuals.R#236) - On CRAN
    
     19. Testing util functions to sim series for tests (@test_test_utils.R#28) - On CRAN
    
     ══ Failed ══════════════════════════════════════════════════════════════════════
     ── 1. Error: bigglm and my c++ version yields similar results (@test_bigglm_wrap
     no applicable method for 'bigglm' applied to an object of class "function"
     1: suppressWarnings(bigglm_res <- biglm::bigglm(form, get_data_func, family = if (model ==
     "logit") binomial() else poisson())) at testthat/test_bigglm_wrapper.R:266
     2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     3: biglm::bigglm(form, get_data_func, family = if (model == "logit") binomial() else poisson())
     4: biglm::bigglm(form, get_data_func, family = if (model == "logit") binomial() else poisson())
    
     ── 2. Error: bigglm and my c++ version yields similar results with offsets (@tes
     no applicable method for 'bigglm' applied to an object of class "function"
     1: suppressWarnings(bigglm_res <- biglm::bigglm(form, get_data_func, family = if (model ==
     "logit") binomial() else poisson())) at testthat/test_bigglm_wrapper.R:285
     2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     3: biglm::bigglm(form, get_data_func, family = if (model == "logit") binomial() else poisson())
     4: biglm::bigglm(form, get_data_func, family = if (model == "logit") binomial() else poisson())
    
     ── 3. Error: bigglm and my c++ version yields similar with weights (@test_bigglm
     no applicable method for 'bigglm' applied to an object of class "function"
     1: suppressWarnings(bigglm_res <- biglm::bigglm(form, get_data_func, family = if (model ==
     "logit") binomial() else poisson(), weights = ~ws)) at testthat/test_bigglm_wrapper.R:308
     2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     3: biglm::bigglm(form, get_data_func, family = if (model == "logit") binomial() else poisson(),
     weights = ~ws)
     4: biglm::bigglm(form, get_data_func, family = if (model == "logit") binomial() else poisson(),
     weights = ~ws)
    
     ── 4. Error: Only fixed effects yields same results as bigglm with logit model (
     no applicable method for 'bigglm' applied to an object of class "data.frame"
     1: suppressWarnings(res2 <- bigglm(update(form, Y ~ . - ddFixed_intercept()), data = tmp_design$X,
     family = binomial(), chunksize = 1000)) at testthat/test_fixed_effects_in_M_step.R:24
     2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     3: bigglm(update(form, Y ~ . - ddFixed_intercept()), data = tmp_design$X, family = binomial(),
     chunksize = 1000)
     4: bigglm(update(form, Y ~ . - ddFixed_intercept()), data = tmp_design$X, family = binomial(),
     chunksize = 1000)
    
     ── 5. Error: Only fixed effects yields same results as bigglm with exponential m
     no applicable method for 'bigglm' applied to an object of class "data.frame"
     1: suppressWarnings(res2 <- bigglm(update(form, Y ~ . - ddFixed_intercept() + offset(log(pmin(tstop,
     t) - pmax(tstart, t - 1)))), data = tmp_design$X, family = poisson(), chunksize = 1000,
     tolerance = 1e-04)) at testthat/test_fixed_effects_in_M_step.R:65
     2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     3: bigglm(update(form, Y ~ . - ddFixed_intercept() + offset(log(pmin(tstop, t) - pmax(tstart,
     t - 1)))), data = tmp_design$X, family = poisson(), chunksize = 1000, tolerance = 1e-04)
     4: bigglm(update(form, Y ~ . - ddFixed_intercept() + offset(log(pmin(tstop, t) - pmax(tstart,
     t - 1)))), data = tmp_design$X, family = poisson(), chunksize = 1000, tolerance = 1e-04)
    
     ── 6. Error: Only fixed effects yields same results as bigglm with exponential m
     no applicable method for 'bigglm' applied to an object of class "data.frame"
     1: suppressWarnings(res2 <- bigglm(update(form, Y ~ . - ddFixed_intercept() + offset(log(pmin(tstop,
     t) - pmax(tstart, t - 1)))), data = tmp_design$X, family = poisson(), chunksize = 1000,
     tolerance = 1e-04, weights = ~ws)) at testthat/test_fixed_effects_in_M_step.R:207
     2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     3: bigglm(update(form, Y ~ . - ddFixed_intercept() + offset(log(pmin(tstop, t) - pmax(tstart,
     t - 1)))), data = tmp_design$X, family = poisson(), chunksize = 1000, tolerance = 1e-04,
     weights = ~ws)
     4: bigglm(update(form, Y ~ . - ddFixed_intercept() + offset(log(pmin(tstop, t) - pmax(tstart,
     t - 1)))), data = tmp_design$X, family = poisson(), chunksize = 1000, tolerance = 1e-04,
     weights = ~ws)
    
     ══ DONE ════════════════════════════════════════════════════════════════════════
     Error: Test failures
     Execution halted
Flavor: r-release-linux-x86_64