Last updated on 2026-07-29 20:56:40 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 14.46 | 336.35 | 350.81 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 8.74 | 220.85 | 229.59 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 24.00 | 476.70 | 500.70 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 10.00 | 202.64 | 212.64 | ERROR | |
| r-devel-windows-x86_64 | 1.0.0 | 17.00 | 302.00 | 319.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.0 | 17.07 | 327.21 | 344.28 | ERROR | |
| r-release-linux-x86_64 | 1.0.0 | 12.71 | 330.46 | 343.17 | ERROR | |
| r-release-macos-arm64 | 1.0.0 | 3.00 | 85.00 | 88.00 | OK | |
| r-release-macos-x86_64 | 1.0.0 | 10.00 | 313.00 | 323.00 | OK | |
| r-release-windows-x86_64 | 1.0.0 | 19.00 | 314.00 | 333.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.0.0 | 3.00 | 87.00 | 90.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.0 | 10.00 | 310.00 | 320.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.0 | 23.00 | 419.00 | 442.00 | ERROR |
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-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [111s/174s]
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=4030642 on localhost:11564 at 11:08:23.272
starting worker pid=4030643 on localhost:11564 at 11:08:23.331
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Loading required package: simDAG
loaded simDAG and set parent environment
loaded simDAG and set parent environment
Attaching package: ‘data.table’
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Loading required package: foreach
Attaching package: ‘data.table’
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starting worker pid=4032640 on localhost:11564 at 11:08:28.109
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loaded simDAG and set parent environment
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loaded simDAG and set parent environment
Attaching package: ‘data.table’
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%notin%
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starting worker pid=4034212 on localhost:11564 at 11:08:33.859
starting worker pid=4034213 on localhost:11564 at 11:08:33.888
Loading required package: simDAG
loaded simDAG and set parent environment
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loaded simDAG and set parent environment
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%notin%
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starting worker pid=4035924 on localhost:11564 at 11:08:40.390
starting worker pid=4035923 on localhost:11564 at 11:08:40.499
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loaded simDAG and set parent environment
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Loading required package: foreach
Loading required package: rngtools
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starting worker pid=4037185 on localhost:11564 at 11:08:46.252
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Loading required package: simDAG
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loaded simDAG and set parent environment
Attaching package: ‘data.table’
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|
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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-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [67s/100s]
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=1130992 on localhost:11496 at 19:47:12.489
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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-gcc
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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [175s/251s]
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=643180 on localhost:11859 at 15:25:45.947
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loaded simDAG and set parent environment
Attaching package: ‘data.table’
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Attaching package: ‘data.table’
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Loading required package: foreach
Loading required package: rngtools
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Loading required package: rngtools
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Attaching package: ‘data.table’
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Loading required package: simDAG
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loaded simDAG and set parent environment
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Attaching package: ‘data.table’
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Loading required package: foreach
Loading required package: rngtools
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-linux-x86_64-fedora-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-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [68s/86s]
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=3924910 on localhost:11094 at 13:45:05.532
starting worker pid=3924911 on localhost:11094 at 13:45:05.537
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
Loading required package: simDAG
Attaching package: ‘data.table’
loaded simDAG and set parent environment
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
|
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|=============================================================== | 90%
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|======================================================================| 100%starting worker pid=3925715 on localhost:11094 at 13:45:07.841
starting worker pid=3925714 on localhost:11094 at 13:45:07.848
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%
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: foreach
Loading required package: rngtools
Loading required package: rngtools
starting worker pid=3927063 on localhost:11094 at 13:45:11.031
starting worker pid=3927064 on localhost:11094 at 13:45:11.037
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%
Attaching package: ‘data.table’
Loading required package: foreach
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
Loading required package: rngtools
starting worker pid=3929745 on localhost:11094 at 13:45:14.555
starting worker pid=3929746 on localhost:11094 at 13:45:14.557
|
| | 0%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%
Loading required package: foreach
loaded simDAG and set parent environment
Loading required package: rngtools
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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|
|============== | 20%
|
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|
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|
|======================================================================| 100%starting worker pid=3930059 on localhost:11094 at 13:45:17.486
starting worker pid=3930060 on localhost:11094 at 13:45:17.489
|
| | 0%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: rngtools
Loading required package: foreach
Loading required package: rngtools
|
|=================================== | 50%
|
|======================================================================| 100%starting worker pid=3930654 on localhost:11094 at 13:45:19.982
starting worker pid=3930655 on localhost:11094 at 13:45:19.984
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
Loading required package: simDAG
Attaching package: ‘data.table’
loaded simDAG and set parent environment
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: rngtools
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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [104s]
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=71200 on localhost:11529 at 16:17:28.827
starting worker pid=22564 on localhost:11529 at 16:17:28.843
|
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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'
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|======================================================================| 100%starting worker pid=88452 on localhost:11529 at 16:17:31.504
starting worker pid=45312 on localhost:11529 at 16:17:31.511
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loaded simDAG and set parent environment
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%notin%
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loaded simDAG and set parent environment
Attaching package: 'data.table'
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%notin%
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starting worker pid=51412 on localhost:11529 at 16:17:34.866
starting worker pid=15768 on localhost:11529 at 16:17:34.880
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loaded simDAG and set parent environment
Attaching package: 'data.table'
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loaded simDAG and set parent environment
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%notin%
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starting worker pid=104724 on localhost:11529 at 16:17:38.525
starting worker pid=31020 on localhost:11529 at 16:17:38.539
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
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%notin%
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loaded simDAG and set parent environment
Attaching package: 'data.table'
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%notin%
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|
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|======================================================================| 100%starting worker pid=61064 on localhost:11529 at 16:17:41.512
starting worker pid=20812 on localhost:11529 at 16:17:41.520
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
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%notin%
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loaded simDAG and set parent environment
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|
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|
|======================================================================| 100%starting worker pid=30912 on localhost:11529 at 16:17:44.160
starting worker pid=70460 on localhost:11529 at 16:17:44.184
|
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loaded simDAG and set parent environment
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%notin%
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loaded simDAG and set parent environment
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|
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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-windows-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [107s/160s]
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=438150 on localhost:11788 at 22:14:22.730
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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
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [107s/171s]
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=2786841 on localhost:11771 at 22:14:24.299
starting worker pid=2786840 on localhost:11771 at 22:14:24.405
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loaded simDAG and set parent environment
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%notin%
loaded simDAG and set parent environment
Loading required package: foreach
Loading required package: rngtools
Attaching package: ‘data.table’
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%notin%
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|======================================================================| 100%starting worker pid=2788106 on localhost:11771 at 22:14:28.904
starting worker pid=2788105 on localhost:11771 at 22:14:28.908
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loaded simDAG and set parent environment
loaded simDAG and set parent environment
Attaching package: ‘data.table’
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%notin%
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Loading required package: foreach
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%notin%
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Loading required package: rngtools
Loading required package: rngtools
starting worker pid=2790604 on localhost:11771 at 22:14:36.087
starting worker pid=2790605 on localhost:11771 at 22:14:36.104
Loading required package: simDAG
Loading required package: simDAG
loaded simDAG and set parent environment
loaded simDAG and set parent environment
Attaching package: ‘data.table’
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%notin%
Attaching package: ‘data.table’
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%notin%
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Loading required package: foreach
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Loading required package: rngtools
starting worker pid=2792619 on localhost:11771 at 22:14:43.428
starting worker pid=2792620 on localhost:11771 at 22:14:43.515
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%notin%
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|======================================================================| 100%starting worker pid=2794157 on localhost:11771 at 22:14:48.901
starting worker pid=2794156 on localhost:11771 at 22:14:48.911
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Loading required package: simDAG
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Loading required package: rngtools
loaded simDAG and set parent environment
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%notin%
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|
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|======================================================================| 100%starting worker pid=2796903 on localhost:11771 at 22:14:52.994
starting worker pid=2796904 on localhost:11771 at 22:14:53.112
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loaded simDAG and set parent environment
Loading required package: simDAG
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%notin%
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loaded simDAG and set parent environment
Loading required package: rngtools
Attaching package: ‘data.table’
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%notin%
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|
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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-release-linux-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=114548 on localhost:11476 at 19:57:15.142
starting worker pid=60964 on localhost:11476 at 19:57:15.149
|
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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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%notin%
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loaded simDAG and set parent environment
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%notin%
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starting worker pid=102988 on localhost:11476 at 19:57:21.380
starting worker pid=69848 on localhost:11476 at 19:57:21.413
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loaded simDAG and set parent environment
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loaded simDAG and set parent environment
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%notin%
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starting worker pid=36952 on localhost:11476 at 19:57:24.723
starting worker pid=108416 on localhost:11476 at 19:57:24.756
|
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loaded simDAG and set parent environment
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%notin%
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loaded simDAG and set parent environment
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%notin%
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|
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|======================================================================| 100%starting worker pid=48288 on localhost:11476 at 19:57:28.010
starting worker pid=62048 on localhost:11476 at 19:57:28.017
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
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%notin%
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loaded simDAG and set parent environment
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%notin%
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|
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starting worker pid=78932 on localhost:11476 at 19:57:30.680
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loaded simDAG and set parent environment
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%notin%
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loaded simDAG and set parent environment
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%notin%
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|
|=================================== | 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-release-windows-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [157s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(simDAG)
> library(testthat)
> library(data.table)
> 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=35860 on localhost:11251 at 07:16:42.111
starting worker pid=105444 on localhost:11251 at 07:16:42.134
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starting worker pid=107484 on localhost:11251 at 07:16:45.893
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starting worker pid=25152 on localhost:11251 at 07:16:50.840
starting worker pid=38836 on localhost:11251 at 07:16:50.843
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loaded simDAG and set parent environment
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loaded simDAG and set parent environment
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starting worker pid=2680 on localhost:11251 at 07:16:56.048
starting worker pid=17664 on localhost:11251 at 07:16:56.111
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starting worker pid=29592 on localhost:11251 at 07:17:00.676
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loaded simDAG and set parent environment
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|======================================================================| 100%starting worker pid=67416 on localhost:11251 at 07:17:04.266
starting worker pid=91928 on localhost:11251 at 07:17:04.293
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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-oldrel-windows-x86_64