• using R version 4.6.1 (2026-06-24 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: 2026-07-21 15:08:33 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 See the install log for details.
• 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 ... [15s] 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 ... [8s] 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 ... [109s] ERROR   Running 'testthat.R' [108s] 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=30956 on localhost:11302 at 17:11:23.144   starting worker pid=34444 on localhost:11302 at 17:11:23.182        |     | | 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=17260 on localhost:11302 at 17:11:25.748   starting worker pid=10596 on localhost:11302 at 17:11:25.770   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=55092 on localhost:11302 at 17:11:29.317   starting worker pid=33664 on localhost:11302 at 17:11:29.342   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=10760 on localhost:11302 at 17:11:32.974   starting worker pid=29720 on localhost:11302 at 17:11:33.021        |     | | 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=9788 on localhost:11302 at 17:11:36.261   starting worker pid=31264 on localhost:11302 at 17:11:36.270        |     | | 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=37532 on localhost:11302 at 17:11:39.087   starting worker pid=12688 on localhost:11302 at 17:11:39.126        |     | | 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 ... [78s] 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/rlang_error> 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 ... [20s] OK
• DONE

Status: 3 ERRORs