CRAN Package Check Results for Package serodynamics

Last updated on 2026-11-10 15:53:40 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	0.1.0	8.32	111.98	120.30	ERROR
r-devel-linux-x86_64-debian-gcc	0.1.0	6.36	80.13	86.49	ERROR
r-devel-linux-x86_64-fedora-clang	0.1.0	7.00	78.86	85.86	OK
r-devel-linux-x86_64-fedora-gcc	0.1.0	7.00	83.73	90.73	OK
r-devel-windows-x86_64	0.1.0	12.00	133.00	145.00	OK
r-patched-linux-x86_64	0.1.0				OK
r-release-linux-x86_64	0.1.0	8.52	103.14	111.66	OK
r-release-macos-arm64	0.1.0	2.00	39.00	41.00	OK
r-release-macos-x86_64	0.1.0	7.00	151.00	158.00	OK
r-release-windows-x86_64	0.1.0	12.00	123.00	135.00	OK
r-oldrel-macos-arm64	0.1.0	2.00	39.00	41.00	OK
r-oldrel-macos-x86_64	0.1.0	6.00	126.00	132.00	OK
r-oldrel-windows-x86_64	0.1.0	16.00	157.00	173.00	OK

Check Details

Version: 0.1.0
Check: examples
Result: ERROR Running examples in ‘serodynamics-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: postprocess_jags_output > ### Title: Postprocess JAGS output > ### Aliases: postprocess_jags_output > > ### ** Examples > > set.seed(1) > raw_data <- + serocalculator::typhoid_curves_nostrat_100 |> + dplyr::filter( + antigen_iso |> stringr::str_starts(pattern = "HlyE") + ) |> + sim_case_data( + n = 5, + antigen_isos = c("HlyE_IgA", "HlyE_IgG") + ) > prepped_data <- prep_data(raw_data) > priors <- prep_priors(max_antigens = prepped_data$n_antigen_isos) > nchains <- 2 > # nr of MC chains to run simultaneously > nadapt <- 100 > # nr of iterations for adaptation > nburnin <- 100 > # nr of iterations to use for burn-in > nmc <- 100 > # nr of samples in posterior chains > niter <- 100 > # nr of iterations for posterior sample > nthin <- round(niter / nmc) > # thinning needed to produce nmc from niter > > tomonitor <- c("y0", "y1", "t1", "alpha", "shape") > > file_mod <- serodynamics_example("model.jags") > > set.seed(11325) > jags_post <- runjags::run.jags( + model = file_mod, + data = c(prepped_data, priors), + inits = initsfunction, + method = "parallel", + adapt = nadapt, + burnin = nburnin, + thin = nthin, + sample = nmc, + n.chains = nchains, + monitor = tomonitor, + summarise = FALSE + ) Warning in structure(c(0, 0, 0, 0, 0, 5, 6, 7, 8, NA, 6, 30, 13, 14, 14, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(0.301489, -0.0462667, -0.351521, -0.252303, -0.214489, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(1, 1, 7, 7, 1, 1, -4, -4, -1, -1), .Dim = c(2, 5)) : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1e-05, 1e-05, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 50, 50, 0, 0, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(4, 4, 1, 1), .Dim = c(2, 2)) : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(0, 0, 0, 0, 0, 5, 6, 7, 8, NA, 6, 30, 13, 14, 14, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(0.301489, -0.0462667, -0.351521, -0.252303, -0.214489, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(1, 1, 7, 7, 1, 1, -4, -4, -1, -1), .Dim = c(2, 5)) : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1e-05, 1e-05, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 50, 50, 0, 0, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(4, 4, 1, 1), .Dim = c(2, 2)) : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Calling 2 simulations using the parallel method... Following the progress of chain 1 (the program will wait for all chains to finish before continuing): Welcome to JAGS 5.0.1 on Tue Nov 10 11:35:00 2026 JAGS is free software and comes with ABSOLUTELY NO WARRANTY Loading module: basemod: ok Loading module: bugs: ok Loading module: diag: ok . . Reading data file data.txt . Compiling model graph Resolving undeclared variables Allocating nodes Graph information: Fully observed stochastic nodes: 42 Unobserved stochastic nodes: 24 Total graph size: 930 . Reading parameter file inits1.txt . Initializing model Error in node (log(((y1[1,2]^(1-shape[1,2]))-((1-shape[1,2])*alpha[1,2]*(smpl.t[1,1]-t1[1,2]))))) Invalid parent values at model initialization Deleting model . Adaptation skipped: model is not in adaptive mode. . Updating 100 -------------------------------------------------| 100 Can't update. No model! Deleting model . Can't set monitor. No model! . Can't set monitor. No model! . Can't set monitor. No model! . Can't set monitor. No model! . Can't set monitor. No model! . Updating 100 -------------------------------------------------| 100 Can't update. No model! Deleting model . No model . Can't dump CODA output. No model! . Can't dump samplers. No model! . Updating 0 Can't update. No model! Deleting model . Deleting model . Exiting JAGS All chains have finished Note: the model did not require adaptation Error in runjags.readin(directory = startinfo$directory, silent.jags = silent.jags, : All the simulations appear to have crashed - check the model output in failed.jags() for clues Calls: <Anonymous> -> extend.jags -> runjags.readin Note: Either one or more simulation(s) failed, or there was an error in processing the results. You may be able to retrieve any successful simulations using: results.jags("/home/hornik/tmp/scratch/RtmpS1gaHb/runjagsfiles3f34506c307357", recover.chains=TRUE) See the help file for that function for possible options. To remove failed simulation folders use cleanup.jags() - this will be run automatically when the runjags package is unloaded Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_predicted_curve 5.558 0.104 7.026 Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘dobson.Rmd’ using rmarkdown Quitting from dobson.Rmd:17-22 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `library()`: ! there is no package called 'rjags' --- Backtrace: ▆ 1. └─base::library(rjags) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'dobson.Rmd' failed with diagnostics: there is no package called 'rjags' --- failed re-building ‘dobson.Rmd’ SUMMARY: processing the following file failed: ‘dobson.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.1.0
Check: examples
Result: ERROR Running examples in ‘serodynamics-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: postprocess_jags_output > ### Title: Postprocess JAGS output > ### Aliases: postprocess_jags_output > > ### ** Examples > > set.seed(1) > raw_data <- + serocalculator::typhoid_curves_nostrat_100 |> + dplyr::filter( + antigen_iso |> stringr::str_starts(pattern = "HlyE") + ) |> + sim_case_data( + n = 5, + antigen_isos = c("HlyE_IgA", "HlyE_IgG") + ) > prepped_data <- prep_data(raw_data) > priors <- prep_priors(max_antigens = prepped_data$n_antigen_isos) > nchains <- 2 > # nr of MC chains to run simultaneously > nadapt <- 100 > # nr of iterations for adaptation > nburnin <- 100 > # nr of iterations to use for burn-in > nmc <- 100 > # nr of samples in posterior chains > niter <- 100 > # nr of iterations for posterior sample > nthin <- round(niter / nmc) > # thinning needed to produce nmc from niter > > tomonitor <- c("y0", "y1", "t1", "alpha", "shape") > > file_mod <- serodynamics_example("model.jags") > > set.seed(11325) > jags_post <- runjags::run.jags( + model = file_mod, + data = c(prepped_data, priors), + inits = initsfunction, + method = "parallel", + adapt = nadapt, + burnin = nburnin, + thin = nthin, + sample = nmc, + n.chains = nchains, + monitor = tomonitor, + summarise = FALSE + ) Warning in structure(c(0, 0, 0, 0, 0, 5, 6, 7, 8, NA, 6, 30, 13, 14, 14, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(0.301489, -0.0462667, -0.351521, -0.252303, -0.214489, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(1, 1, 7, 7, 1, 1, -4, -4, -1, -1), .Dim = c(2, 5)) : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1e-05, 1e-05, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 50, 50, 0, 0, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(4, 4, 1, 1), .Dim = c(2, 2)) : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(0, 0, 0, 0, 0, 5, 6, 7, 8, NA, 6, 30, 13, 14, 14, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(0.301489, -0.0462667, -0.351521, -0.252303, -0.214489, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(1, 1, 7, 7, 1, 1, -4, -4, -1, -1), .Dim = c(2, 5)) : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1e-05, 1e-05, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 50, 50, 0, 0, : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Warning in structure(c(4, 4, 1, 1), .Dim = c(2, 2)) : Replacing special names ‘.Dim’ is deprecated; use ‘dim’ instead. Calling 2 simulations using the parallel method... Following the progress of chain 1 (the program will wait for all chains to finish before continuing): Welcome to JAGS 5.0.1 on Mon Nov 9 20:22:29 2026 JAGS is free software and comes with ABSOLUTELY NO WARRANTY Loading module: basemod: ok Loading module: bugs: ok Loading module: diag: ok . . Reading data file data.txt . Compiling model graph Resolving undeclared variables Allocating nodes Graph information: Fully observed stochastic nodes: 42 Unobserved stochastic nodes: 24 Total graph size: 930 . Reading parameter file inits1.txt . Initializing model Error in node (log(((y1[1,2]^(1-shape[1,2]))-((1-shape[1,2])*alpha[1,2]*(smpl.t[1,1]-t1[1,2]))))) Invalid parent values at model initialization Deleting model . Adaptation skipped: model is not in adaptive mode. . Updating 100 -------------------------------------------------| 100 Can't update. No model! Deleting model . Can't set monitor. No model! . Can't set monitor. No model! . Can't set monitor. No model! . Can't set monitor. No model! . Can't set monitor. No model! . Updating 100 -------------------------------------------------| 100 Can't update. No model! Deleting model . No model . Can't dump CODA output. No model! . Can't dump samplers. No model! . Updating 0 Can't update. No model! Deleting model . Deleting model . Exiting JAGS All chains have finished Note: the model did not require adaptation Error in runjags.readin(directory = startinfo$directory, silent.jags = silent.jags, : All the simulations appear to have crashed - check the model output in failed.jags() for clues Calls: <Anonymous> -> extend.jags -> runjags.readin Note: Either one or more simulation(s) failed, or there was an error in processing the results. You may be able to retrieve any successful simulations using: results.jags("/home/hornik/tmp/scratch/RtmpdsXI69/runjagsfiles1538a368bc5777", recover.chains=TRUE) See the help file for that function for possible options. To remove failed simulation folders use cleanup.jags() - this will be run automatically when the runjags package is unloaded Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_predicted_curve 3.675 0.114 5.834 Flavor: r-devel-linux-x86_64-debian-gcc