CRAN Package Check Results for Package missingHE

Last updated on 2026-09-04 11:50:17 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.6.1	50.36	590.82	641.18	OK
r-devel-linux-x86_64-debian-gcc	1.6.1	30.24	387.93	418.17	OK
r-devel-linux-x86_64-fedora-clang	1.6.1	37.00	379.67	416.67	OK
r-devel-linux-x86_64-fedora-gcc	1.6.1	36.00	411.69	447.69	OK
r-devel-windows-x86_64	1.6.1	50.00	503.00	553.00	ERROR
r-patched-linux-x86_64	1.6.1	49.13	569.97	619.10	OK
r-release-linux-x86_64	1.6.1	48.57	572.97	621.54	OK
r-release-macos-arm64	1.6.1	13.00	116.00	129.00	OK
r-release-macos-x86_64	1.6.1	38.00	528.00	566.00	OK
r-release-windows-x86_64	1.6.1	50.00	532.00	582.00	OK
r-oldrel-macos-arm64	1.6.1	13.00	127.00	140.00	OK
r-oldrel-macos-x86_64	1.6.1	37.00	497.00	534.00	OK
r-oldrel-windows-x86_64	1.6.1	68.00	757.00	825.00	OK

Check Details

Version: 1.6.1
Check: examples
Result: ERROR Running examples in 'missingHE-Ex.R' failed The error most likely occurred in: > ### Name: hurdle > ### Title: Full Bayesian Models to handle missingness in Economic > ### Evaluations (Hurdle Models) > ### Aliases: hurdle > ### Keywords: CEA Hurdle JAGS Models data missing > > ### ** Examples > > # Quck example to run using subset of MenSS dataset > MenSS.subset <- MenSS[50:100, ] > > # Run the model using the hurdle function assuming a SCAR mechanism > # Use only 100 iterations to run a quick check > model.hurdle <- hurdle(data = MenSS.subset, model.eff = e ~ trt, model.cost = c ~ trt, + model.se = se ~ 1, model.sc = sc ~ 1, se = 1, sc = 0, dist_e = "norm", dist_c = "norm", + type = "SCAR", n.chains = 2, n.iter = 100) module glm loaded Compiling model graph Resolving undeclared variables Allocating nodes Graph information: Observed stochastic nodes: 60 Unobserved stochastic nodes: 152 Total graph size: 1133 Initializing model Error in ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, : zero-variance series Error in ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, : zero-variance series Error in ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, : zero-variance series Error in ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, : zero-variance series > > # Print the results of the JAGS model > print(model.hurdle) mean sd 2.5% 50% alpha[1,1] 0.8552029 0.04086688 7.65e-01 0.8622504 alpha[2,1] 0.0852405 0.08623190 -7.79e-02 0.0965474 alpha[1,2] 1.0000000 0.00000000 1.00e+00 1.0000000 alpha[2,2] 0.0000000 0.00000000 0.00e+00 0.0000000 beta[1,1] 42.7703893 31.47153336 -1.46e+01 42.8872544 beta[2,1] 10.6621597 30.28813438 -3.96e+01 7.5820939 beta[1,2] 0.0000000 0.00000000 0.00e+00 0.0000000 beta[2,2] 0.0000000 0.00000000 0.00e+00 0.0000000 gamma_c -1.2222644 0.74054817 -2.72e+00 -1.1909756 gamma_e -0.3091857 0.47576394 -1.20e+00 -0.2834149 p_c 0.2505798 0.12659831 6.19e-02 0.2330847 p_e 0.4270897 0.11159730 2.32e-01 0.4296181 s_c[1] 231.0436471 50.39006778 1.56e+02 226.9819267 s_c[2] 0.0000100 0.00000000 1.00e-05 0.0000100 s_e[1] 0.1015937 0.02804029 6.06e-02 0.0988762 s_e[2] 0.0000100 0.00000000 1.00e-05 0.0000100 tau_c[1] 0.0000216 0.00000983 9.21e-06 0.0000194 tau_c[2] 9999999999.9999981 0.00000000 1.00e+10 9999999999.9999981 tau_e[1] 118.3102675 60.89067904 3.49e+01 102.2865731 tau_e[2] 9999999999.9999981 0.00000000 1.00e+10 9999999999.9999981 tmu_c 36.0549963 27.18458408 -1.08e+01 36.4539313 tmu_e 0.9422830 0.02451618 8.88e-01 0.9414858 97.5% Rhat n.eff alpha[1,1] 0.949835 1.010 100 alpha[2,1] 0.261970 1.011 100 alpha[1,2] 1.000000 1.000 1 alpha[2,2] 0.000000 1.000 1 beta[1,1] 98.888679 0.997 100 beta[2,1] 80.512288 1.008 100 beta[1,2] 0.000000 1.000 1 beta[2,2] 0.000000 1.000 1 gamma_c 0.146487 1.068 33 gamma_e 0.637111 1.042 100 p_c 0.536554 1.088 28 p_e 0.654020 1.048 100 s_c[1] 329.502862 1.001 100 s_c[2] 0.000010 1.000 1 s_e[1] 0.169542 1.157 13 s_e[2] 0.000010 1.000 1 tau_c[1] 0.000041 1.001 100 tau_c[2] 9999999999.999998 1.000 1 tau_e[1] 272.131989 1.157 13 tau_e[2] 9999999999.999998 1.000 1 tmu_c 89.688508 1.007 100 tmu_e 0.988371 1.005 100 > # > > # Use dic information criterion to assess model fit > pic.dic <- pic(model.hurdle, criterion = "dic", cases = "cc") > pic.dic $d_bar [1] -36.81777 $pD [1] 204.8657 $dic [1] 168.0479 $d_hat [1] -241.6834 > # > > # Extract regression coefficient estimates > coef(model.hurdle) $Effects Mean SD QL QU (Intercept) 0.855 0.041 0.765 0.950 trt2 0.085 0.086 -0.078 0.262 $Costs Mean SD QL QU (Intercept) 42.770 31.472 -14.618 98.889 trt2 10.662 30.288 -39.607 80.512 > # > > ## Don't show: > # Use waic information criterion to assess model fit > pic.waic <- pic(model.hurdle, criterion = "waic", cases = "cc") > pic.waic $elpd [1] 15.42885 $elpd_se [1] 40.56594 $p [1] 5.266018 $p_se [1] 0.6281658 $waic [1] -30.8577 $waic_se [1] 81.13187 $pointwise elpd_waic p_waic waic [1,] 18.586768 0.3551583 -37.173536 [2,] -6.502173 0.1919359 13.004346 [3,] -6.303347 0.2478219 12.606694 [4,] 1.604880 0.2168823 -3.209761 [5,] -7.151715 0.4138777 14.303431 [6,] 9.172790 0.5041855 -18.345579 [7,] -7.919465 0.3696665 15.838930 [8,] -7.487206 0.4795243 14.974413 [9,] 18.586768 0.3551583 -37.173536 [10,] 2.929572 0.1750029 -5.859143 [11,] -6.198919 0.1878427 12.397837 [12,] -6.604574 0.4736046 13.209148 [13,] 18.586768 0.3551583 -37.173536 [14,] 2.931216 0.1793959 -5.862431 [15,] -8.802512 0.7608026 17.605023 > ## End(Don't show) > > # Assess model convergence using graphical tools > # Produce histograms of the posterior samples for the mean effects > diag.hist <- diagnostic(model.hurdle, type = "histogram", param = "mu.e") Loading required namespace: ggmcmc Failed with error: 'object 'ggcoef_multinom' is not exported by 'namespace:ggstats'' Error in diagnostic(model.hurdle, type = "histogram", param = "mu.e") : You need to install the R packages 'ggmcmc', 'coda' and 'mcmcr'. Please run in your R terminal: install.packages('ggmcmc', 'coda', 'mcmcr') Execution halted Flavor: r-devel-windows-x86_64

Version: 1.6.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'Fitting_MNAR_models_in_missingHE.Rmd' using rmarkdown --- finished re-building 'Fitting_MNAR_models_in_missingHE.Rmd' --- re-building 'Introduction_to_missingHE.Rmd' using rmarkdown Warning in eng_r(options) : Failed to tidy R code in chunk 'diag1'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Failed with error: 'object 'ggcoef_multinom' is not exported by 'namespace:ggstats'' Quitting from Introduction_to_missingHE.Rmd:326-328 [fig2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `diagnostic()`: ! You need to install the R packages 'ggmcmc', 'coda' and 'mcmcr'. Please run in your R terminal: install.packages('ggmcmc', 'coda', 'mcmcr') --- Backtrace: ▆ 1. └─missingHE::diagnostic(x = sm1_mar, type = "traceplot", param = "sd.e") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Introduction_to_missingHE.Rmd' failed with diagnostics: You need to install the R packages 'ggmcmc', 'coda' and 'mcmcr'. Please run in your R terminal: install.packages('ggmcmc', 'coda', 'mcmcr') --- failed re-building 'Introduction_to_missingHE.Rmd' --- re-building 'Longitudinal_models_in_missingHE.Rmd' using rmarkdown Warning in eng_r(options) : Failed to tidy R code in chunk 'diag1'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Failed with error: 'object 'ggcoef_multinom' is not exported by 'namespace:ggstats'' Quitting from Longitudinal_models_in_missingHE.Rmd:225-227 [fig2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `diagnostic()`: ! You need to install the R packages 'ggmcmc', 'coda' and 'mcmcr'. Please run in your R terminal: install.packages('ggmcmc', 'coda', 'mcmcr') --- Backtrace: ▆ 1. └─missingHE::diagnostic(x = lmdm1_mar, type = "denplot", param = "beta.f") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Longitudinal_models_in_missingHE.Rmd' failed with diagnostics: You need to install the R packages 'ggmcmc', 'coda' and 'mcmcr'. Please run in your R terminal: install.packages('ggmcmc', 'coda', 'mcmcr') --- failed re-building 'Longitudinal_models_in_missingHE.Rmd' --- re-building 'Model_customisation_in_missingHE.Rmd' using rmarkdown Warning in eng_r(options) : Failed to tidy R code in chunk 'selprint'. Reason: Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. Failed with error: 'object 'ggcoef_multinom' is not exported by 'namespace:ggstats'' Quitting from Model_customisation_in_missingHE.Rmd:228-230 [figplotdiag] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `diagnostic()`: ! You need to install the R packages 'ggmcmc', 'coda' and 'mcmcr'. Please run in your R terminal: install.packages('ggmcmc', 'coda', 'mcmcr') --- Backtrace: ▆ 1. └─missingHE::diagnostic(x = sm1_nn_cov, type = "acf", param = "alpha") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Model_customisation_in_missingHE.Rmd' failed with diagnostics: You need to install the R packages 'ggmcmc', 'coda' and 'mcmcr'. Please run in your R terminal: install.packages('ggmcmc', 'coda', 'mcmcr') --- failed re-building 'Model_customisation_in_missingHE.Rmd' SUMMARY: processing the following files failed: 'Introduction_to_missingHE.Rmd' 'Longitudinal_models_in_missingHE.Rmd' 'Model_customisation_in_missingHE.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-devel-windows-x86_64