* using log directory 'd:/Rcompile/CRANpkg/local/4.7/simDAG.Rcheck' * using R Under development (unstable) (2026-07-16 r90264 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * current time: 2026-07-17 20:45:46 UTC * checking for file 'simDAG/DESCRIPTION' ... OK * this is package 'simDAG' version '1.0.0' * 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 'simDAG' can be installed ... OK * checking installed package size ... 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 ... [2s] OK * checking whether the package can be loaded with stated dependencies ... [2s] OK * checking whether the package can be unloaded cleanly ... [2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s] OK * checking whether the namespace can be unloaded cleanly ... [2s] OK * checking loading without being on the library search path ... [2s] 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 ... [18s] OK * checking Rd files ... [2s] 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [9s] ERROR Running examples in 'simDAG-Ex.R' failed The error most likely occurred in: > ### Name: node_binomial > ### Title: Generate Data from a (Mixed) Binomial Regression Model > ### Aliases: node_binomial > > ### ** Examples > > library(simDAG) > > set.seed(5425) > > # define needed DAG > dag <- empty_dag() + + node("age", type="rnorm", mean=50, sd=4) + + node("sex", type="rbernoulli", p=0.5) + + node("smoking", type="binomial", parents=c("age", "sex"), + betas=c(1.1, 0.4), intercept=-2) > > # define the same DAG, but using a pretty formula > dag <- empty_dag() + + node("age", type="rnorm", mean=50, sd=4) + + node("sex", type="rbernoulli", p=0.5) + + node("smoking", type="binomial", + formula= ~ -2 + age*1.1 + sexTRUE*0.4) > > # simulate data from it > sim_dat <- sim_from_dag(dag=dag, n_sim=100) > > # returning only the estimated probability instead > dag <- empty_dag() + + node("age", type="rnorm", mean=50, sd=4) + + node("sex", type="rbernoulli", p=0.5) + + node("smoking", type="binomial", parents=c("age", "sex"), + betas=c(1.1, 0.4), intercept=-2, return_prob=TRUE) > > sim_dat <- sim_from_dag(dag=dag, n_sim=100) > > ## an example using a random effect > if (requireNamespace("simr")) { + + library(simr) + + dag_mixed <- empty_dag() + + node("School", type="rcategorical", probs=rep(0.1, 10), + labels=LETTERS[1:10]) + + node("Age", type="rnorm", mean=12, sd=2) + + node("Grade", type="binomial", formula= ~ -10 + Age*1.2 + (1|School), + var_corr=0.3) + + sim_dat <- sim_from_dag(dag=dag_mixed, n_sim=100) + } Loading required namespace: simr Loading required package: lme4 Loading required package: Matrix Attaching package: 'simr' The following object is masked from 'package:lme4': getData Error: An error occured when processing node 'Grade'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [111s] ERROR Running 'testthat.R' [111s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(simDAG) > library(testthat) > library(data.table) Attaching package: 'data.table' The following object is masked from 'package:base': %notin% > library(igraph) Attaching package: 'igraph' The following object is masked from 'package:testthat': compare The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union > library(ggdag) Attaching package: 'ggdag' The following object is masked from 'package:stats': filter > > data.table::setDTthreads(1) > > test_check("simDAG") Saving _problems/test_node_lmer-21.R Saving _problems/test_node_lmer-52.R Saving _problems/test_node_lmer-85.R Saving _problems/test_node_lmer-116.R Saving _problems/test_node_lmer-148.R Saving _problems/test_node_lmer-178.R Saving _problems/test_node_lmer-208.R Saving _problems/test_node_lmer-239.R Saving _problems/test_node_lmer-272.R Saving _problems/test_node_lmer-393.R Saving _problems/test_node_zeroinfl-114.R t = 1 node = sickness2 t = 1 node = sickness1 t = 2 node = sickness2 t = 2 node = sickness1 t = 3 node = sickness2 t = 3 node = sickness1 t = 4 node = sickness2 t = 4 node = sickness1 t = 5 node = sickness2 t = 5 node = sickness1 starting worker pid=31128 on localhost:11756 at 22:48:41.165 starting worker pid=24988 on localhost:11756 at 22:48:41.216 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%starting worker pid=40636 on localhost:11756 at 22:48:43.849 starting worker pid=4488 on localhost:11756 at 22:48:43.855 Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools starting worker pid=47508 on localhost:11756 at 22:48:47.337 starting worker pid=63916 on localhost:11756 at 22:48:47.359 Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools starting worker pid=7904 on localhost:11756 at 22:48:51.098 starting worker pid=65980 on localhost:11756 at 22:48:51.099 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 100%starting worker pid=94276 on localhost:11756 at 22:48:54.217 starting worker pid=45504 on localhost:11756 at 22:48:54.235 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools | |=================================== | 50% | |======================================================================| 100%starting worker pid=38864 on localhost:11756 at 22:48:57.076 starting worker pid=82056 on localhost:11756 at 22:48:57.102 | | | 0%Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools Loading required package: simDAG loaded simDAG and set parent environment Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Loading required package: foreach Loading required package: rngtools | |=================================== | 50% | |======================================================================| 100%[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ] ══ Skipped tests (56) ══════════════════════════════════════════════════════════ • On CRAN (56): 'test_DAG.network_S3.r:4:1', 'test_DAG.network_S3.r:10:1', 'test_DAG.network_S3.r:18:1', 'test_DAG.network_S3.r:24:1', 'test_DAG.network_S3.r:32:1', 'test_DAG.network_S3.r:44:1', 'test_DAG.network_S3.r:50:1', 'test_DAG.network_S3.r:58:1', 'test_DAG.network_S3.r:64:1', 'test_DAG.network_S3.r:72:1', 'test_DAG.node_S3.r:4:1', 'test_DAG.node_S3.r:9:1', 'test_DAG.node_S3.r:14:1', 'test_DAG.node_S3.r:19:1', 'test_DAG.node_S3.r:24:1', 'test_DAG.node_S3.r:32:1', 'test_DAG.node_S3.r:37:1', 'test_DAG.node_S3.r:42:1', 'test_DAG.node_S3.r:47:1', 'test_DAG.node_S3.r:52:1', 'test_dag.r:14:1', 'test_dag.r:21:1', 'test_dag.r:34:1', 'test_dag.r:44:1', 'test_dag.r:51:1', 'test_dag.r:64:1', 'test_node.r:548:1', 'test_node_rsurv.r:99:3', 'test_plot.DAG.r:11:1', 'test_plot.DAG.r:15:1', 'test_plot.DAG.r:19:1', 'test_plot.DAG.r:23:1', 'test_plot.DAG.r:27:1', 'test_plot.DAG.r:31:1', 'test_plot.DAG.r:35:1', 'test_plot.DAG.r:40:1', 'test_plot.DAG.r:44:1', 'test_plot.DAG.r:52:1', 'test_plot.DAG.r:59:1', 'test_plot.DAG.r:64:1', 'test_plot.DAG.r:69:1', 'test_plot.DAG.r:100:1', 'test_plot.DAG.r:104:1', 'test_plot.DAG.r:108:1', 'test_plot.simDT.r:24:1', 'test_plot.simDT.r:28:1', 'test_plot.simDT.r:32:1', 'test_plot.simDT.r:36:1', 'test_plot.simDT.r:40:1', 'test_plot.simDT.r:48:1', 'test_plot.simDT.r:56:1', 'test_simDT_S3.r:11:1', 'test_simDT_S3.r:15:1', 'test_simDT_S3.r:20:1', 'test_simDT_S3.r:25:1', 'test_sim_discrete_event.r:693:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_node_lmer.r:21:3'): simple random effect ─────────────────────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:21:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:52:3'): simple random effect in disrete-time simulation ── Error: An error occured when processing node 'Y' at time t = 1. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_discrete_time(...) at test_node_lmer.r:52:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:85:3'): simple random effect + categorical fixed effect ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:85:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:116:3'): simple random effect + interaction effect ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:116:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:148:3'): simple random effect + interaction effect of categorical vars ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:148:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:178:3'): simple random effect + cubic terms ──────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:178:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:208:3'): simple random effect + ONLY cubic terms ─── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:208:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:239:3'): multiple random effects ─────────────────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=2, npar=2, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:239:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:272:3'): with random effects and random slopes ───── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=3, npar=3, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:272:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_lmer.r:393:3'): simple random effect with non-default link ── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:393:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ── Error ('test_node_zeroinfl.r:114:3'): with random effects ─────────────────── Error: An error occured when processing node 'Y'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_zeroinfl.r:114:3 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) [ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [80s] ERROR Error(s) in re-building vignettes: --- re-building 'simDAG.Rmd' using rmarkdown --- finished re-building 'simDAG.Rmd' --- re-building 'v_cookbook.Rmd' using rmarkdown Quitting from v_cookbook.Rmd:132-140 [unnamed-chunk-7] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! An error occured when processing node 'Outcome'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) --- Backtrace: ▆ 1. └─simDAG::sim_from_dag(dag, n_sim = 1000) 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'v_cookbook.Rmd' failed with diagnostics: An error occured when processing node 'Outcome'. The message was: Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0) --- failed re-building 'v_cookbook.Rmd' --- re-building 'v_covid_example.Rmd' using rmarkdown --- finished re-building 'v_covid_example.Rmd' --- re-building 'v_custom_nodes.Rmd' using rmarkdown --- finished re-building 'v_custom_nodes.Rmd' --- re-building 'v_sim_discrete_event.Rmd' using rmarkdown --- finished re-building 'v_sim_discrete_event.Rmd' --- re-building 'v_sim_discrete_time.Rmd' using rmarkdown --- finished re-building 'v_sim_discrete_time.Rmd' --- re-building 'v_sim_from_dag.Rmd' using rmarkdown --- finished re-building 'v_sim_from_dag.Rmd' --- re-building 'v_sim_networks.Rmd' using rmarkdown --- finished re-building 'v_sim_networks.Rmd' --- re-building 'v_using_formulas.Rmd' using rmarkdown --- finished re-building 'v_using_formulas.Rmd' SUMMARY: processing the following file failed: 'v_cookbook.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [23s] OK * checking HTML version of manual ... [21s] OK * DONE Status: 3 ERRORs