Last updated on 2026-07-21 17:50:09 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 12.98 | 347.80 | 360.78 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 10.28 | 249.17 | 259.45 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 25.00 | 271.37 | 296.37 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 220.06 | ERROR | |||
| r-devel-windows-x86_64 | 1.0.0 | 15.00 | 300.00 | 315.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.0 | 16.49 | 351.52 | 368.01 | OK | |
| r-release-linux-x86_64 | 1.0.0 | 13.81 | 335.14 | 348.95 | 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 | 15.00 | 314.00 | 329.00 | 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 | 424.00 | 447.00 | 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-release-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [110s/173s]
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=3704276 on localhost:11597 at 11:03:29.900
starting worker pid=3704277 on localhost:11597 at 11:03:29.970
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loaded simDAG and set parent environment
Attaching package: ‘data.table’
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Loading required package: foreach
Loading required package: rngtools
Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: ‘data.table’
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Loading required package: simDAG
Attaching package: ‘data.table’
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loaded simDAG and set parent environment
Loading required package: rngtools
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%notin%
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starting worker pid=3708417 on localhost:11597 at 11:03:41.911
starting worker pid=3708416 on localhost:11597 at 11:03:41.937
Loading required package: simDAG
Loading required package: simDAG
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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Loading required package: rngtools
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loaded simDAG and set parent environment
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Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: ‘data.table’
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Attaching package: ‘data.table’
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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-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-release-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [74s/118s]
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=3872227 on localhost:11377 at 19:46:47.904
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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’ [86s/105s]
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=2136879 on localhost:11311 at 09:41:23.194
starting worker pid=2136880 on localhost:11311 at 09:41:23.205
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Loading required package: rngtools
loaded simDAG and set parent environment
Attaching package: ‘data.table’
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Loading required package: rngtools
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starting worker pid=2137938 on localhost:11311 at 09:41:37.509
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starting worker pid=2137998 on localhost:11311 at 09:41:40.578
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loaded simDAG and set parent environment
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Loading required package: rngtools
|
|=================================== | 50%
|
|======================================================================| 100%[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ]
══ Skipped tests (56) ══════════════════════════════════════════════════════════
• On CRAN (56): 'test_DAG.network_S3.r:4:1', 'test_DAG.network_S3.r:10:1',
'test_DAG.network_S3.r:18:1', 'test_DAG.network_S3.r:24:1',
'test_DAG.network_S3.r:32:1', 'test_DAG.network_S3.r:44:1',
'test_DAG.network_S3.r:50:1', 'test_DAG.network_S3.r:58:1',
'test_DAG.network_S3.r:64:1', 'test_DAG.network_S3.r:72:1',
'test_DAG.node_S3.r:4:1', 'test_DAG.node_S3.r:9:1',
'test_DAG.node_S3.r:14:1', 'test_DAG.node_S3.r:19:1',
'test_DAG.node_S3.r:24:1', 'test_DAG.node_S3.r:32:1',
'test_DAG.node_S3.r:37:1', 'test_DAG.node_S3.r:42:1',
'test_DAG.node_S3.r:47:1', 'test_DAG.node_S3.r:52:1', 'test_dag.r:14:1',
'test_dag.r:21:1', 'test_dag.r:34:1', 'test_dag.r:44:1', 'test_dag.r:51:1',
'test_dag.r:64:1', 'test_node.r:548:1', 'test_node_rsurv.r:99:3',
'test_plot.DAG.r:11:1', 'test_plot.DAG.r:15:1', 'test_plot.DAG.r:19:1',
'test_plot.DAG.r:23:1', 'test_plot.DAG.r:27:1', 'test_plot.DAG.r:31:1',
'test_plot.DAG.r:35:1', 'test_plot.DAG.r:40:1', 'test_plot.DAG.r:44:1',
'test_plot.DAG.r:52:1', 'test_plot.DAG.r:59:1', 'test_plot.DAG.r:64:1',
'test_plot.DAG.r:69:1', 'test_plot.DAG.r:100:1', 'test_plot.DAG.r:104:1',
'test_plot.DAG.r:108:1', 'test_plot.simDT.r:24:1', 'test_plot.simDT.r:28:1',
'test_plot.simDT.r:32:1', 'test_plot.simDT.r:36:1', 'test_plot.simDT.r:40:1',
'test_plot.simDT.r:48:1', 'test_plot.simDT.r:56:1', 'test_simDT_S3.r:11:1',
'test_simDT_S3.r:15:1', 'test_simDT_S3.r:20:1', 'test_simDT_S3.r:25:1',
'test_sim_discrete_event.r:693:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_node_lmer.r:21:3'): simple random effect ───────────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:21:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:52:3'): simple random effect in disrete-time simulation ──
Error: An error occured when processing node 'Y' at time t = 1. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_discrete_time(...) at test_node_lmer.r:52:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:85:3'): simple random effect + categorical fixed effect ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:85:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:116:3'): simple random effect + interaction effect ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:116:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:148:3'): simple random effect + interaction effect of categorical vars ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:148:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:178:3'): simple random effect + cubic terms ────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:178:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:208:3'): simple random effect + ONLY cubic terms ───
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:208:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:239:3'): multiple random effects ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=2, npar=2, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:239:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:272:3'): with random effects and random slopes ─────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=3, npar=3, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:272:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:393:3'): simple random effect with non-default link ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:393:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_zeroinfl.r:114:3'): with random effects ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_zeroinfl.r:114:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-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/85s]
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=2272933 on localhost:11435 at 08:51:46.835
starting worker pid=2272934 on localhost:11435 at 08:51:46.851
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loaded simDAG and set parent environment
Loading required package: simDAG
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
loaded simDAG and set parent environment
Loading required package: foreach
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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|======================================================================| 100%starting worker pid=2273861 on localhost:11435 at 08:51:49.213
starting worker pid=2273860 on localhost:11435 at 08:51:49.225
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%
loaded simDAG and set parent environment
Loading required package: foreach
Attaching package: ‘data.table’
Loading required package: rngtools
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
starting worker pid=2274882 on localhost:11435 at 08:51:52.283
starting worker pid=2274883 on localhost:11435 at 08:51:52.298
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
starting worker pid=2275781 on localhost:11435 at 08:51:55.734
starting worker pid=2275782 on localhost:11435 at 08:51:55.745
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Loading required package: simDAG
loaded simDAG and set parent environment
loaded simDAG and set parent environment
Attaching package: ‘data.table’
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
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
|
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|======================================================================| 100%starting worker pid=2276756 on localhost:11435 at 08:51:58.994
starting worker pid=2276755 on localhost:11435 at 08:51:59.001
|
| | 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%
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
|
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|======================================================================| 100%starting worker pid=2277203 on localhost:11435 at 08:52:01.497
starting worker pid=2277205 on localhost:11435 at 08:52:01.502
|
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loaded simDAG and set parent environment
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
|
|=================================== | 50%
|
|======================================================================| 100%[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ]
══ Skipped tests (56) ══════════════════════════════════════════════════════════
• On CRAN (56): 'test_DAG.network_S3.r:4:1', 'test_DAG.network_S3.r:10:1',
'test_DAG.network_S3.r:18:1', 'test_DAG.network_S3.r:24:1',
'test_DAG.network_S3.r:32:1', 'test_DAG.network_S3.r:44:1',
'test_DAG.network_S3.r:50:1', 'test_DAG.network_S3.r:58:1',
'test_DAG.network_S3.r:64:1', 'test_DAG.network_S3.r:72:1',
'test_DAG.node_S3.r:4:1', 'test_DAG.node_S3.r:9:1',
'test_DAG.node_S3.r:14:1', 'test_DAG.node_S3.r:19:1',
'test_DAG.node_S3.r:24:1', 'test_DAG.node_S3.r:32:1',
'test_DAG.node_S3.r:37:1', 'test_DAG.node_S3.r:42:1',
'test_DAG.node_S3.r:47:1', 'test_DAG.node_S3.r:52:1', 'test_dag.r:14:1',
'test_dag.r:21:1', 'test_dag.r:34:1', 'test_dag.r:44:1', 'test_dag.r:51:1',
'test_dag.r:64:1', 'test_node.r:548:1', 'test_node_rsurv.r:99:3',
'test_plot.DAG.r:11:1', 'test_plot.DAG.r:15:1', 'test_plot.DAG.r:19:1',
'test_plot.DAG.r:23:1', 'test_plot.DAG.r:27:1', 'test_plot.DAG.r:31:1',
'test_plot.DAG.r:35:1', 'test_plot.DAG.r:40:1', 'test_plot.DAG.r:44:1',
'test_plot.DAG.r:52:1', 'test_plot.DAG.r:59:1', 'test_plot.DAG.r:64:1',
'test_plot.DAG.r:69:1', 'test_plot.DAG.r:100:1', 'test_plot.DAG.r:104:1',
'test_plot.DAG.r:108:1', 'test_plot.simDT.r:24:1', 'test_plot.simDT.r:28:1',
'test_plot.simDT.r:32:1', 'test_plot.simDT.r:36:1', 'test_plot.simDT.r:40:1',
'test_plot.simDT.r:48:1', 'test_plot.simDT.r:56:1', 'test_simDT_S3.r:11:1',
'test_simDT_S3.r:15:1', 'test_simDT_S3.r:20:1', 'test_simDT_S3.r:25:1',
'test_sim_discrete_event.r:693:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_node_lmer.r:21:3'): simple random effect ───────────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:21:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:52:3'): simple random effect in disrete-time simulation ──
Error: An error occured when processing node 'Y' at time t = 1. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_discrete_time(...) at test_node_lmer.r:52:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:85:3'): simple random effect + categorical fixed effect ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:85:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:116:3'): simple random effect + interaction effect ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:116:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:148:3'): simple random effect + interaction effect of categorical vars ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:148:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:178:3'): simple random effect + cubic terms ────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:178:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:208:3'): simple random effect + ONLY cubic terms ───
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:208:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:239:3'): multiple random effects ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=2, npar=2, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:239:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:272:3'): with random effects and random slopes ─────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=3, npar=3, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:272:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:393:3'): simple random effect with non-default link ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:393:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_zeroinfl.r:114:3'): with random effects ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_zeroinfl.r:114:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [105s]
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=81260 on localhost:11458 at 09:42:07.830
starting worker pid=33204 on localhost:11458 at 09:42:07.849
|
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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=29344 on localhost:11458 at 09:42:10.467
starting worker pid=80736 on localhost:11458 at 09:42:10.502
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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=26796 on localhost:11458 at 09:42:13.691
starting worker pid=75616 on localhost:11458 at 09:42:13.698
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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=7780 on localhost:11458 at 09:42:17.255
starting worker pid=57316 on localhost:11458 at 09:42:17.274
|
| | 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=64796 on localhost:11458 at 09:42:20.491
starting worker pid=34104 on localhost:11458 at 09:42:20.511
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
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loaded simDAG and set parent environment
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|
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|======================================================================| 100%starting worker pid=38408 on localhost:11458 at 09:42:23.221
starting worker pid=81204 on localhost:11458 at 09:42:23.270
|
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loaded simDAG and set parent environment
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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/158s]
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
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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' [110s]
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=62768 on localhost:11015 at 12:49:58.961
starting worker pid=66340 on localhost:11015 at 12:49:58.986
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loaded simDAG and set parent environment
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starting worker pid=39412 on localhost:11015 at 12:50:05.132
starting worker pid=105328 on localhost:11015 at 12:50:05.150
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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=90456 on localhost:11015 at 12:50:08.790
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starting worker pid=34636 on localhost:11015 at 12:50:12.105
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|======================================================================| 100%starting worker pid=107708 on localhost:11015 at 12:50:14.930
starting worker pid=35124 on localhost:11015 at 12:50:14.945
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%notin%
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|======================================================================| 100%[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ]
══ Skipped tests (56) ══════════════════════════════════════════════════════════
• On CRAN (56): 'test_DAG.network_S3.r:4:1', 'test_DAG.network_S3.r:10:1',
'test_DAG.network_S3.r:18:1', 'test_DAG.network_S3.r:24:1',
'test_DAG.network_S3.r:32:1', 'test_DAG.network_S3.r:44:1',
'test_DAG.network_S3.r:50:1', 'test_DAG.network_S3.r:58:1',
'test_DAG.network_S3.r:64:1', 'test_DAG.network_S3.r:72:1',
'test_DAG.node_S3.r:4:1', 'test_DAG.node_S3.r:9:1',
'test_DAG.node_S3.r:14:1', 'test_DAG.node_S3.r:19:1',
'test_DAG.node_S3.r:24:1', 'test_DAG.node_S3.r:32:1',
'test_DAG.node_S3.r:37:1', 'test_DAG.node_S3.r:42:1',
'test_DAG.node_S3.r:47:1', 'test_DAG.node_S3.r:52:1', 'test_dag.r:14:1',
'test_dag.r:21:1', 'test_dag.r:34:1', 'test_dag.r:44:1', 'test_dag.r:51:1',
'test_dag.r:64:1', 'test_node.r:548:1', 'test_node_rsurv.r:99:3',
'test_plot.DAG.r:11:1', 'test_plot.DAG.r:15:1', 'test_plot.DAG.r:19:1',
'test_plot.DAG.r:23:1', 'test_plot.DAG.r:27:1', 'test_plot.DAG.r:31:1',
'test_plot.DAG.r:35:1', 'test_plot.DAG.r:40:1', 'test_plot.DAG.r:44:1',
'test_plot.DAG.r:52:1', 'test_plot.DAG.r:59:1', 'test_plot.DAG.r:64:1',
'test_plot.DAG.r:69:1', 'test_plot.DAG.r:100:1', 'test_plot.DAG.r:104:1',
'test_plot.DAG.r:108:1', 'test_plot.simDT.r:24:1', 'test_plot.simDT.r:28:1',
'test_plot.simDT.r:32:1', 'test_plot.simDT.r:36:1', 'test_plot.simDT.r:40:1',
'test_plot.simDT.r:48:1', 'test_plot.simDT.r:56:1', 'test_simDT_S3.r:11:1',
'test_simDT_S3.r:15:1', 'test_simDT_S3.r:20:1', 'test_simDT_S3.r:25:1',
'test_sim_discrete_event.r:693:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_node_lmer.r:21:3'): simple random effect ───────────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:21:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:52:3'): simple random effect in disrete-time simulation ──
Error: An error occured when processing node 'Y' at time t = 1. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_discrete_time(...) at test_node_lmer.r:52:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:85:3'): simple random effect + categorical fixed effect ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:85:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:116:3'): simple random effect + interaction effect ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:116:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:148:3'): simple random effect + interaction effect of categorical vars ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:148:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:178:3'): simple random effect + cubic terms ────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:178:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:208:3'): simple random effect + ONLY cubic terms ───
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:208:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:239:3'): multiple random effects ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=2, npar=2, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:239:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:272:3'): with random effects and random slopes ─────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=3, npar=3, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:272:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:393:3'): simple random effect with non-default link ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:393:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_zeroinfl.r:114:3'): with random effects ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_zeroinfl.r:114:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ]
Error:
! Test failures.
Execution halted
Flavor: r-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=13176 on localhost:11903 at 20:49:57.168
starting worker pid=4112 on localhost:11903 at 20:49:57.169
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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=19480 on localhost:11903 at 20:50:10.546
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|
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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-oldrel-windows-x86_64