Last updated on 2026-08-04 02:51:12 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 13.96 | 336.20 | 350.16 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 10.24 | 250.22 | 260.46 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 14.00 | 280.49 | 294.49 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 207.91 | OK | |||
| r-devel-windows-x86_64 | 1.0.0 | 16.00 | 303.00 | 319.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.0 | 16.75 | 327.79 | 344.54 | ERROR | |
| r-release-linux-x86_64 | 1.0.1 | 12.19 | 356.65 | 368.84 | OK | |
| r-release-macos-arm64 | 1.0.1 | 3.00 | 82.00 | 85.00 | OK | |
| r-release-macos-x86_64 | 1.0.1 | 10.00 | 315.00 | 325.00 | OK | |
| r-release-windows-x86_64 | 1.0.1 | 16.00 | 337.00 | 353.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.1 | 3.00 | 88.00 | 91.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.1 | 10.00 | 506.00 | 516.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.1 | 22.00 | 458.00 | 480.00 | OK |
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘simDAG-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [109s/172s]
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=2131454 on localhost:11940 at 11:10:14.921
starting worker pid=2131455 on localhost:11940 at 11:10:15.033
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loaded simDAG and set parent environment
Attaching package: ‘data.table’
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Loading required package: simDAG
Loading required package: foreach
Loading required package: rngtools
loaded simDAG and set parent environment
Attaching package: ‘data.table’
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loaded simDAG and set parent environment
Attaching package: ‘data.table’
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starting worker pid=2135067 on localhost:11940 at 11:10:26.364
starting worker pid=2135066 on localhost:11940 at 11:10:26.483
Loading required package: simDAG
loaded simDAG and set parent environment
Loading required package: simDAG
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loaded simDAG and set parent environment
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starting worker pid=2137687 on localhost:11940 at 11:10:34.854
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loaded simDAG and set parent environment
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loaded simDAG and set parent environment
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loaded simDAG and set parent environment
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Attaching package: ‘data.table’
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|======================================================================| 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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.0
Check: re-building of vignette outputs
Result: 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
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64
Version: 1.0.0
Check: examples
Result: 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
Flavor: r-devel-windows-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [107s]
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=92912 on localhost:11980 at 14:19:46.342
starting worker pid=63184 on localhost:11980 at 14:19:46.346
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| | 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
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|======================================================================| 100%starting worker pid=113416 on localhost:11980 at 14:19:48.903
starting worker pid=20020 on localhost:11980 at 14:19:48.919
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=48672 on localhost:11980 at 14:19:52.240
starting worker pid=97304 on localhost:11980 at 14:19:52.270
Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: 'data.table'
The following object is masked from 'package:base':
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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=35724 on localhost:11980 at 14:19:55.939
starting worker pid=74396 on localhost:11980 at 14:19:55.955
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loaded simDAG and set parent environment
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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':
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|======================================================================| 100%starting worker pid=48228 on localhost:11980 at 14:19:59.114
starting worker pid=90800 on localhost:11980 at 14:19:59.173
|
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loaded simDAG and set parent environment
Attaching package: 'data.table'
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|
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|======================================================================| 100%starting worker pid=112076 on localhost:11980 at 14:20:01.888
starting worker pid=103252 on localhost:11980 at 14:20:01.909
|
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loaded simDAG and set parent environment
Attaching package: 'data.table'
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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':
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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
Flavor: r-devel-windows-x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: 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
Flavor: r-devel-windows-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [104s/156s]
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=809398 on localhost:11861 at 22:19:42.653
starting worker pid=809399 on localhost:11861 at 22:19:42.776
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loaded simDAG and set parent environment
Loading required package: simDAG
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
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
|
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|======================================================================| 100%starting worker pid=810305 on localhost:11861 at 22:19:46.870
starting worker pid=810306 on localhost:11861 at 22:19:46.909
Loading required package: simDAG
Loading required package: simDAG
loaded simDAG and set parent environment
loaded simDAG and set parent environment
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
Loading required package: rngtools
starting worker pid=811892 on localhost:11861 at 22:19:52.741
starting worker pid=811893 on localhost:11861 at 22:19:52.786
Loading required package: simDAG
loaded simDAG and set parent environment
Loading required package: simDAG
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
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|======================================================================| 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
Flavor: r-patched-linux-x86_64