* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/Markovchart.Rcheck’ * using R Under development (unstable) (2025-12-20 r89211) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘Markovchart/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Markovchart’ version ‘2.1.5’ * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Markovchart’ can be installed ... OK * 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * 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 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 ... [11s/11s] OK * checking Rd files ... NOTE checkRd: (-1) Markovchart.Rd:154: Lost braces 154 | If either \code{h} or \code{k} have length greater than 1, then the \code{G-value} (weighted average of average cost and cost standard deviation) is calculated for all given values without optimisation. The value of the function in this case is a data frame of class code{Markov_grid} with \code{length(h)*length(k)} number of rows and three columns for \code{h}, \code{k} and the \code{G-value}. | ^ * checking Rd metadata ... OK * checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking examples with --run-donttest ... [3s/32s] ERROR Running examples in ‘Markovchart-Ex.R’ failed The error most likely occurred in: > ### Name: LDL > ### Title: Aggregated low-density-lipoprotein patient data for control > ### chart applications > ### Aliases: LDL > ### Keywords: datasets > > ### ** Examples > > #Print data > data("LDL") > LDL target_value standard_deviation expected_shift_size num_exp_daily_shifts 1 3 0.1 0.2666667 0.008333333 rep_size_first rep_size_second samp_prob_first samp_prob_second sampling_cost 1 0.027 1.15 0.1 30 5.012871 OOC_cost base_rep_cost prop_rep_cost 1 4.598446 9.971323 7.478492 > > ### > > # Run analysis from Dobi & Zempleni 2019. > # Note that the code below is generated with updated HUF-EUR rate and > # a more accurate R implementation than in the original paper. > > stat_LDL_cost <- Markovstat( + shiftfun = 'exp', h = 50, k = 3.15-LDL$target_value, + sigma = LDL$standard_deviation, + s = LDL$num_exp_daily_shifts, + delta = LDL$expected_shift_size, + RanRep = TRUE, alpha = LDL$rep_size_first, beta = LDL$rep_size_second, + RanSam = TRUE, q = LDL$samp_prob_first, z = LDL$samp_prob_second, + Vd = 100, V = 6-LDL$target_value) > ## No test: > #Defining parallel_opt parallel settings. > #parallel_opt can also be left empty to be defined automatically by the function. > require(parallel) Loading required package: parallel > num_workers <- min(c(detectCores(),2)) > parall <- list(cl=makeCluster(num_workers), forward=FALSE, loginfo=TRUE) > res_LDL_cost <- Markovchart( + statdist = stat_LDL_cost, + OPTIM = TRUE, p = 1, + cs = LDL$sampling_cost, + cf = LDL$base_rep_cost, + coparams = c(0,LDL$OOC_cost), + crparams = c(LDL$base_rep_cost,LDL$prop_rep_cost), + parallel_opt = parall) > > num_workers <- min(c(detectCores(),2)) > parall <- list(cl=makeCluster(num_workers), forward=FALSE, loginfo=TRUE) > res_LDL_cost_grid <- Markovchart( + statdist = stat_LDL_cost, + h=seq(50,75,2.5), + k=seq(0.05,0.25,0.02), + p = 1, + cs = LDL$sampling_cost, + cf = LDL$base_rep_cost, + coparams = c(0,LDL$OOC_cost), + crparams = c(LDL$base_rep_cost,LDL$prop_rep_cost), + parallel_opt = parall) > > require(ggplot2) Loading required package: ggplot2 > plot(res_LDL_cost_grid, + y = 'Expected \ndaily cost', + mid = '#ff9494', + high = '#800000', + xlab = 'Days between samplings', + ylab = 'Critical LDL increase') + + geom_point(aes(x = res_LDL_cost$Parameters[[1]], + y = res_LDL_cost$Parameters[[2]])) Error in `geom_text_contour()`: ! Problem while converting geom to grob. ℹ Error occurred in the 3rd layer. Caused by error in `[.data.table`: ! attempt access index 18/18 in VECTOR_ELT Backtrace: ▆ 1. ├─base (local) ``(x) 2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x) 3. │ ├─ggplot2::ggplot_gtable(data) 4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data) 5. │ └─ggplot2:::by_layer(...) 6. │ ├─rlang::try_fetch(...) 7. │ │ ├─base::tryCatch(...) 8. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 9. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 11. │ │ └─base::withCallingHandlers(...) 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 13. │ └─l$draw_geom(d, layout) 14. │ └─ggplot2 (local) draw_geom(..., self = self) 15. │ └─self$geom$draw_layer(...) 16. │ └─ggplot2 (local) draw_layer(..., self = self) 17. │ └─base::lapply(...) 18. │ └─ggplot2 (local) FUN(X[[i]], ...) 19. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params)) 20. │ └─self$draw_panel(...) 21. │ └─metR (local) draw_panel(...) 22. │ ├─data[, `:=`(N, .N), by = .(group, piece)] 23. │ └─data.table:::`[.data.table`(...) 24. └─base::.handleSimpleError(...) 25. └─rlang (local) h(simpleError(msg, call)) 26. └─handlers[[1L]](cnd) 27. └─cli::cli_abort(...) 28. └─rlang::abort(...) Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [11s/22s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘Applications.Rmd’ using rmarkdown Time between samplings (h) 1 55.7 Critical value (k) 1 0.158 Expected cost 1 0.43 Cost sd due to process var. 1 0.5 Quitting from Applications.Rmd:90-110 [app_LDL_cost_plot] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `geom_text_contour()`: ! Problem while converting geom to grob. ℹ Error occurred in the 3rd layer. Caused by error in `[.data.table`: ! attempt access index 18/18 in VECTOR_ELT --- Backtrace: ▆ 1. ├─base::withVisible(knit_print(x, ...)) 2. ├─knitr::knit_print(x, ...) 3. └─knitr:::knit_print.default(x, ...) 4. └─knitr::normal_print(x) 5. ├─base::print(x) 6. └─ggplot2 (local) `print.ggplot2::ggplot`(x) 7. ├─ggplot2::ggplot_gtable(data) 8. └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data) 9. └─ggplot2:::by_layer(...) 10. ├─rlang::try_fetch(...) 11. │ ├─base::tryCatch(...) 12. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 13. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 15. │ └─base::withCallingHandlers(...) 16. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 17. └─l$draw_geom(d, layout) 18. └─ggplot2 (local) draw_geom(..., self = self) 19. └─self$geom$draw_layer(...) 20. └─ggplot2 (local) draw_layer(..., self = self) 21. └─base::lapply(...) 22. └─ggplot2 (local) FUN(X[[i]], ...) 23. ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params)) 24. └─self$draw_panel(...) 25. └─metR (local) draw_panel(...) 26. ├─data[, `:=`(N, .N), by = .(group, piece)] 27. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Applications.Rmd' failed with diagnostics: Problem while converting geom to grob. ℹ Error occurred in the 3rd layer. Caused by error in `[.data.table`: ! attempt access index 18/18 in VECTOR_ELT --- failed re-building ‘Applications.Rmd’ SUMMARY: processing the following file failed: ‘Applications.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/data/blackswan/ripley/R/packages/tests-devel/Markovchart.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 2:08.03, 68.77 + 16.90