Last updated on 2026-08-01 01:53:01 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 13.96 | 336.20 | 350.16 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 9.97 | 222.39 | 232.36 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 23.00 | 294.67 | 317.67 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 10.00 | 206.93 | 216.93 | OK | |
| r-devel-windows-x86_64 | 1.0.0 | 16.00 | 303.00 | 319.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.0 | 16.75 | 327.79 | 344.54 | ERROR | |
| r-release-linux-x86_64 | 1.0.0 | 12.71 | 330.46 | 343.17 | ERROR | |
| r-release-macos-arm64 | 1.0.1 | 3.00 | 82.00 | 85.00 | OK | |
| r-release-macos-x86_64 | 1.0.1 | 10.00 | 315.00 | 325.00 | OK | |
| r-release-windows-x86_64 | 1.0.0 | 16.00 | 311.00 | 327.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.0.1 | 3.00 | 88.00 | 91.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.1 | 10.00 | 506.00 | 516.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.1 | 13.00 | 377.00 | 390.00 | ERROR |
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘simDAG-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: node_binomial
> ### Title: Generate Data from a (Mixed) Binomial Regression Model
> ### Aliases: node_binomial
>
> ### ** Examples
>
> library(simDAG)
>
> set.seed(5425)
>
> # define needed DAG
> dag <- empty_dag() +
+ node("age", type="rnorm", mean=50, sd=4) +
+ node("sex", type="rbernoulli", p=0.5) +
+ node("smoking", type="binomial", parents=c("age", "sex"),
+ betas=c(1.1, 0.4), intercept=-2)
>
> # define the same DAG, but using a pretty formula
> dag <- empty_dag() +
+ node("age", type="rnorm", mean=50, sd=4) +
+ node("sex", type="rbernoulli", p=0.5) +
+ node("smoking", type="binomial",
+ formula= ~ -2 + age*1.1 + sexTRUE*0.4)
>
> # simulate data from it
> sim_dat <- sim_from_dag(dag=dag, n_sim=100)
>
> # returning only the estimated probability instead
> dag <- empty_dag() +
+ node("age", type="rnorm", mean=50, sd=4) +
+ node("sex", type="rbernoulli", p=0.5) +
+ node("smoking", type="binomial", parents=c("age", "sex"),
+ betas=c(1.1, 0.4), intercept=-2, return_prob=TRUE)
>
> sim_dat <- sim_from_dag(dag=dag, n_sim=100)
>
> ## an example using a random effect
> if (requireNamespace("simr")) {
+
+ library(simr)
+
+ dag_mixed <- empty_dag() +
+ node("School", type="rcategorical", probs=rep(0.1, 10),
+ labels=LETTERS[1:10]) +
+ node("Age", type="rnorm", mean=12, sd=2) +
+ node("Grade", type="binomial", formula= ~ -10 + Age*1.2 + (1|School),
+ var_corr=0.3)
+
+ sim_dat <- sim_from_dag(dag=dag_mixed, n_sim=100)
+ }
Loading required namespace: simr
Loading required package: lme4
Loading required package: Matrix
Attaching package: ‘simr’
The following object is masked from ‘package:lme4’:
getData
Error: An error occured when processing node 'Grade'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [109s/172s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(simDAG)
> library(testthat)
> library(data.table)
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
> library(igraph)
Attaching package: 'igraph'
The following object is masked from 'package:testthat':
compare
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
> library(ggdag)
Attaching package: 'ggdag'
The following object is masked from 'package:stats':
filter
>
> data.table::setDTthreads(1)
>
> test_check("simDAG")
Saving _problems/test_node_lmer-21.R
Saving _problems/test_node_lmer-52.R
Saving _problems/test_node_lmer-85.R
Saving _problems/test_node_lmer-116.R
Saving _problems/test_node_lmer-148.R
Saving _problems/test_node_lmer-178.R
Saving _problems/test_node_lmer-208.R
Saving _problems/test_node_lmer-239.R
Saving _problems/test_node_lmer-272.R
Saving _problems/test_node_lmer-393.R
Saving _problems/test_node_zeroinfl-114.R
t = 1 node = sickness2
t = 1 node = sickness1
t = 2 node = sickness2
t = 2 node = sickness1
t = 3 node = sickness2
t = 3 node = sickness1
t = 4 node = sickness2
t = 4 node = sickness1
t = 5 node = sickness2
t = 5 node = sickness1
starting worker pid=2131454 on localhost:11940 at 11:10:14.921
starting worker pid=2131455 on localhost:11940 at 11:10:15.033
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loaded simDAG and set parent environment
Attaching package: ‘data.table’
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%notin%
Loading required package: simDAG
Loading required package: foreach
Loading required package: rngtools
loaded simDAG and set parent environment
Attaching package: ‘data.table’
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%notin%
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starting worker pid=2132925 on localhost:11940 at 11:10:19.725
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loaded simDAG and set parent environment
Attaching package: ‘data.table’
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Attaching package: ‘data.table’
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%notin%
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Loading required package: foreach
Loading required package: rngtools
starting worker pid=2135067 on localhost:11940 at 11:10:26.364
starting worker pid=2135066 on localhost:11940 at 11:10:26.483
Loading required package: simDAG
loaded simDAG and set parent environment
Loading required package: simDAG
Attaching package: ‘data.table’
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%notin%
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loaded simDAG and set parent environment
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%notin%
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Loading required package: rngtools
starting worker pid=2137686 on localhost:11940 at 11:10:34.765
starting worker pid=2137687 on localhost:11940 at 11:10:34.854
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loaded simDAG and set parent environment
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Loading required package: rngtools
loaded simDAG and set parent environment
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starting worker pid=2139537 on localhost:11940 at 11:10:40.340
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Loading required package: simDAG
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loaded simDAG and set parent environment
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starting worker pid=2140721 on localhost:11940 at 11:10:45.520
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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’
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%notin%
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Loading required package: foreach
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|
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|
|======================================================================| 100%[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ]
══ Skipped tests (56) ══════════════════════════════════════════════════════════
• On CRAN (56): 'test_DAG.network_S3.r:4:1', 'test_DAG.network_S3.r:10:1',
'test_DAG.network_S3.r:18:1', 'test_DAG.network_S3.r:24:1',
'test_DAG.network_S3.r:32:1', 'test_DAG.network_S3.r:44:1',
'test_DAG.network_S3.r:50:1', 'test_DAG.network_S3.r:58:1',
'test_DAG.network_S3.r:64:1', 'test_DAG.network_S3.r:72:1',
'test_DAG.node_S3.r:4:1', 'test_DAG.node_S3.r:9:1',
'test_DAG.node_S3.r:14:1', 'test_DAG.node_S3.r:19:1',
'test_DAG.node_S3.r:24:1', 'test_DAG.node_S3.r:32:1',
'test_DAG.node_S3.r:37:1', 'test_DAG.node_S3.r:42:1',
'test_DAG.node_S3.r:47:1', 'test_DAG.node_S3.r:52:1', 'test_dag.r:14:1',
'test_dag.r:21:1', 'test_dag.r:34:1', 'test_dag.r:44:1', 'test_dag.r:51:1',
'test_dag.r:64:1', 'test_node.r:548:1', 'test_node_rsurv.r:99:3',
'test_plot.DAG.r:11:1', 'test_plot.DAG.r:15:1', 'test_plot.DAG.r:19:1',
'test_plot.DAG.r:23:1', 'test_plot.DAG.r:27:1', 'test_plot.DAG.r:31:1',
'test_plot.DAG.r:35:1', 'test_plot.DAG.r:40:1', 'test_plot.DAG.r:44:1',
'test_plot.DAG.r:52:1', 'test_plot.DAG.r:59:1', 'test_plot.DAG.r:64:1',
'test_plot.DAG.r:69:1', 'test_plot.DAG.r:100:1', 'test_plot.DAG.r:104:1',
'test_plot.DAG.r:108:1', 'test_plot.simDT.r:24:1', 'test_plot.simDT.r:28:1',
'test_plot.simDT.r:32:1', 'test_plot.simDT.r:36:1', 'test_plot.simDT.r:40:1',
'test_plot.simDT.r:48:1', 'test_plot.simDT.r:56:1', 'test_simDT_S3.r:11:1',
'test_simDT_S3.r:15:1', 'test_simDT_S3.r:20:1', 'test_simDT_S3.r:25:1',
'test_sim_discrete_event.r:693:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_node_lmer.r:21:3'): simple random effect ───────────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:21:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:52:3'): simple random effect in disrete-time simulation ──
Error: An error occured when processing node 'Y' at time t = 1. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_discrete_time(...) at test_node_lmer.r:52:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:85:3'): simple random effect + categorical fixed effect ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:85:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:116:3'): simple random effect + interaction effect ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:116:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:148:3'): simple random effect + interaction effect of categorical vars ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:148:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:178:3'): simple random effect + cubic terms ────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:178:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:208:3'): simple random effect + ONLY cubic terms ───
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:208:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:239:3'): multiple random effects ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=2, npar=2, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:239:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:272:3'): with random effects and random slopes ─────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=3, npar=3, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:272:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:393:3'): simple random effect with non-default link ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:393:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_zeroinfl.r:114:3'): with random effects ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_zeroinfl.r:114:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.0.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘simDAG.Rmd’ using rmarkdown
--- finished re-building ‘simDAG.Rmd’
--- re-building ‘v_cookbook.Rmd’ using rmarkdown
Quitting from v_cookbook.Rmd:132-140 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! An error occured when processing node 'Outcome'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
---
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag, n_sim = 1000)
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'v_cookbook.Rmd' failed with diagnostics:
An error occured when processing node 'Outcome'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
--- failed re-building ‘v_cookbook.Rmd’
--- re-building ‘v_covid_example.Rmd’ using rmarkdown
--- finished re-building ‘v_covid_example.Rmd’
--- re-building ‘v_custom_nodes.Rmd’ using rmarkdown
--- finished re-building ‘v_custom_nodes.Rmd’
--- re-building ‘v_sim_discrete_event.Rmd’ using rmarkdown
--- finished re-building ‘v_sim_discrete_event.Rmd’
--- re-building ‘v_sim_discrete_time.Rmd’ using rmarkdown
--- finished re-building ‘v_sim_discrete_time.Rmd’
--- re-building ‘v_sim_from_dag.Rmd’ using rmarkdown
--- finished re-building ‘v_sim_from_dag.Rmd’
--- re-building ‘v_sim_networks.Rmd’ using rmarkdown
--- finished re-building ‘v_sim_networks.Rmd’
--- re-building ‘v_using_formulas.Rmd’ using rmarkdown
--- finished re-building ‘v_using_formulas.Rmd’
SUMMARY: processing the following file failed:
‘v_cookbook.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [68s/99s]
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")
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Saving _problems/test_node_zeroinfl-114.R
t = 1 node = sickness2
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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: for new files in some other directories
Result: NOTE
Found the following files/directories:
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‘~/tmp/scratch/xvfb-run.0Ho7MD’ ‘~/tmp/scratch/xvfb-run.0vuwNe’
‘~/tmp/scratch/xvfb-run.17Y7Qm’ ‘~/tmp/scratch/xvfb-run.1FlpJj’
‘~/tmp/scratch/xvfb-run.1KWXE7’ ‘~/tmp/scratch/xvfb-run.2gOo6h’
‘~/tmp/scratch/xvfb-run.2mqNRO’ ‘~/tmp/scratch/xvfb-run.3cMAGc’
‘~/tmp/scratch/xvfb-run.3oKpsn’ ‘~/tmp/scratch/xvfb-run.7yBlsD’
‘~/tmp/scratch/xvfb-run.85WTiO’ ‘~/tmp/scratch/xvfb-run.9idYCs’
‘~/tmp/scratch/xvfb-run.A0cXkN’ ‘~/tmp/scratch/xvfb-run.CBvNvi’
‘~/tmp/scratch/xvfb-run.CUyfWx’ ‘~/tmp/scratch/xvfb-run.EVdHos’
‘~/tmp/scratch/xvfb-run.EXl5cy’ ‘~/tmp/scratch/xvfb-run.FCrMEz’
‘~/tmp/scratch/xvfb-run.FTtcdc’ ‘~/tmp/scratch/xvfb-run.Fucayy’
‘~/tmp/scratch/xvfb-run.HuJkRo’ ‘~/tmp/scratch/xvfb-run.HyLjOh’
‘~/tmp/scratch/xvfb-run.J07plh’ ‘~/tmp/scratch/xvfb-run.JdD01A’
‘~/tmp/scratch/xvfb-run.JnoULS’ ‘~/tmp/scratch/xvfb-run.Ke05xd’
‘~/tmp/scratch/xvfb-run.LbPp6V’ ‘~/tmp/scratch/xvfb-run.LxJ21W’
‘~/tmp/scratch/xvfb-run.OCBgis’ ‘~/tmp/scratch/xvfb-run.OLy1Yh’
‘~/tmp/scratch/xvfb-run.PX1lsA’ ‘~/tmp/scratch/xvfb-run.QcxiHO’
‘~/tmp/scratch/xvfb-run.RjLuJ7’ ‘~/tmp/scratch/xvfb-run.T1WMH8’
‘~/tmp/scratch/xvfb-run.T3eNxK’ ‘~/tmp/scratch/xvfb-run.TOROCH’
‘~/tmp/scratch/xvfb-run.TsyeT6’ ‘~/tmp/scratch/xvfb-run.TwQZjB’
‘~/tmp/scratch/xvfb-run.U5gJQV’ ‘~/tmp/scratch/xvfb-run.UCzAWP’
‘~/tmp/scratch/xvfb-run.UJE7ZH’ ‘~/tmp/scratch/xvfb-run.Uv2Xks’
‘~/tmp/scratch/xvfb-run.VMGumd’ ‘~/tmp/scratch/xvfb-run.WBC21g’
‘~/tmp/scratch/xvfb-run.WMKKzo’ ‘~/tmp/scratch/xvfb-run.Y1I7ka’
‘~/tmp/scratch/xvfb-run.YSVHQw’ ‘~/tmp/scratch/xvfb-run.YTj8ZC’
‘~/tmp/scratch/xvfb-run.YtNM8K’ ‘~/tmp/scratch/xvfb-run.Z2Pk70’
‘~/tmp/scratch/xvfb-run.ZpX0FT’ ‘~/tmp/scratch/xvfb-run.cD3fe5’
‘~/tmp/scratch/xvfb-run.cobWCI’ ‘~/tmp/scratch/xvfb-run.cvEZZM’
‘~/tmp/scratch/xvfb-run.dWfxAr’ ‘~/tmp/scratch/xvfb-run.eMwJUl’
‘~/tmp/scratch/xvfb-run.eRtmXD’ ‘~/tmp/scratch/xvfb-run.elA5fG’
‘~/tmp/scratch/xvfb-run.eviaCT’ ‘~/tmp/scratch/xvfb-run.h8YG3k’
‘~/tmp/scratch/xvfb-run.hmflzY’ ‘~/tmp/scratch/xvfb-run.hwAvfG’
‘~/tmp/scratch/xvfb-run.ilV0AM’ ‘~/tmp/scratch/xvfb-run.kOphp2’
‘~/tmp/scratch/xvfb-run.kZAJqL’ ‘~/tmp/scratch/xvfb-run.mB2DCE’
‘~/tmp/scratch/xvfb-run.nR6NWW’ ‘~/tmp/scratch/xvfb-run.nh6Uc5’
‘~/tmp/scratch/xvfb-run.nsljpB’ ‘~/tmp/scratch/xvfb-run.qrx6x8’
‘~/tmp/scratch/xvfb-run.tKbXFw’ ‘~/tmp/scratch/xvfb-run.to3cLM’
‘~/tmp/scratch/xvfb-run.vbH5eK’ ‘~/tmp/scratch/xvfb-run.wNJ19K’
‘~/tmp/scratch/xvfb-run.wuZumw’ ‘~/tmp/scratch/xvfb-run.yi903S’
‘~/tmp/scratch/xvfb-run.z1GC4O’
‘/dev/shm/sm_segment.gimli1.1001.7ec70000.0’
‘~/.cache/pocl/uncached/tempfile_Zzkel2’
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-windows-x86_64, r-release-windows-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [107s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(simDAG)
> library(testthat)
> library(data.table)
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
> library(igraph)
Attaching package: 'igraph'
The following object is masked from 'package:testthat':
compare
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
> library(ggdag)
Attaching package: 'ggdag'
The following object is masked from 'package:stats':
filter
>
> data.table::setDTthreads(1)
>
> test_check("simDAG")
Saving _problems/test_node_lmer-21.R
Saving _problems/test_node_lmer-52.R
Saving _problems/test_node_lmer-85.R
Saving _problems/test_node_lmer-116.R
Saving _problems/test_node_lmer-148.R
Saving _problems/test_node_lmer-178.R
Saving _problems/test_node_lmer-208.R
Saving _problems/test_node_lmer-239.R
Saving _problems/test_node_lmer-272.R
Saving _problems/test_node_lmer-393.R
Saving _problems/test_node_zeroinfl-114.R
t = 1 node = sickness2
t = 1 node = sickness1
t = 2 node = sickness2
t = 2 node = sickness1
t = 3 node = sickness2
t = 3 node = sickness1
t = 4 node = sickness2
t = 4 node = sickness1
t = 5 node = sickness2
t = 5 node = sickness1
starting worker pid=92912 on localhost:11980 at 14:19:46.342
starting worker pid=63184 on localhost:11980 at 14:19:46.346
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loaded simDAG and set parent environment
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loaded simDAG and set parent environment
Attaching package: 'data.table'
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starting worker pid=20020 on localhost:11980 at 14:19:48.919
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loaded simDAG and set parent environment
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%notin%
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starting worker pid=48672 on localhost:11980 at 14:19:52.240
starting worker pid=97304 on localhost:11980 at 14:19:52.270
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loaded simDAG and set parent environment
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starting worker pid=35724 on localhost:11980 at 14:19:55.939
starting worker pid=74396 on localhost:11980 at 14:19:55.955
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loaded simDAG and set parent environment
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starting worker pid=90800 on localhost:11980 at 14:19:59.173
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starting worker pid=103252 on localhost:11980 at 14:20:01.909
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loaded simDAG and set parent environment
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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: 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-windows-x86_64, r-release-windows-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [104s/156s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(simDAG)
> library(testthat)
> library(data.table)
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
> library(igraph)
Attaching package: 'igraph'
The following object is masked from 'package:testthat':
compare
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
> library(ggdag)
Attaching package: 'ggdag'
The following object is masked from 'package:stats':
filter
>
> data.table::setDTthreads(1)
>
> test_check("simDAG")
Saving _problems/test_node_lmer-21.R
Saving _problems/test_node_lmer-52.R
Saving _problems/test_node_lmer-85.R
Saving _problems/test_node_lmer-116.R
Saving _problems/test_node_lmer-148.R
Saving _problems/test_node_lmer-178.R
Saving _problems/test_node_lmer-208.R
Saving _problems/test_node_lmer-239.R
Saving _problems/test_node_lmer-272.R
Saving _problems/test_node_lmer-393.R
Saving _problems/test_node_zeroinfl-114.R
t = 1 node = sickness2
t = 1 node = sickness1
t = 2 node = sickness2
t = 2 node = sickness1
t = 3 node = sickness2
t = 3 node = sickness1
t = 4 node = sickness2
t = 4 node = sickness1
t = 5 node = sickness2
t = 5 node = sickness1
starting worker pid=809398 on localhost:11861 at 22:19:42.653
starting worker pid=809399 on localhost:11861 at 22:19:42.776
|
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loaded simDAG and set parent environment
Loading required package: simDAG
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
loaded simDAG and set parent environment
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
|
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|======================================================================| 100%starting worker pid=810305 on localhost:11861 at 22:19:46.870
starting worker pid=810306 on localhost:11861 at 22:19:46.909
Loading required package: simDAG
Loading required package: simDAG
loaded simDAG and set parent environment
loaded simDAG and set parent environment
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
Loading required package: rngtools
starting worker pid=811892 on localhost:11861 at 22:19:52.741
starting worker pid=811893 on localhost:11861 at 22:19:52.786
Loading required package: simDAG
loaded simDAG and set parent environment
Loading required package: simDAG
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
loaded simDAG and set parent environment
Loading required package: foreach
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
Loading required package: rngtools
starting worker pid=814237 on localhost:11861 at 22:19:59.779
starting worker pid=814238 on localhost:11861 at 22:19:59.813
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
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
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
|
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|======================================================================| 100%starting worker pid=815944 on localhost:11861 at 22:20:05.327
starting worker pid=815943 on localhost:11861 at 22:20:05.362
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
Loading required package: simDAG
Attaching package: ‘data.table’
loaded simDAG and set parent environment
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Attaching package: ‘data.table’
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%notin%
Loading required package: rngtools
Loading required package: foreach
Loading required package: rngtools
|
|=================================== | 50%
|
|======================================================================| 100%starting worker pid=817347 on localhost:11861 at 22:20:09.876
starting worker pid=817348 on localhost:11861 at 22:20:09.964
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: simDAG
Loading required package: rngtools
loaded simDAG and set parent environment
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
|
|=================================== | 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-patched-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [107s/171s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(simDAG)
> library(testthat)
> library(data.table)
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
> library(igraph)
Attaching package: 'igraph'
The following object is masked from 'package:testthat':
compare
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
> library(ggdag)
Attaching package: 'ggdag'
The following object is masked from 'package:stats':
filter
>
> data.table::setDTthreads(1)
>
> test_check("simDAG")
Saving _problems/test_node_lmer-21.R
Saving _problems/test_node_lmer-52.R
Saving _problems/test_node_lmer-85.R
Saving _problems/test_node_lmer-116.R
Saving _problems/test_node_lmer-148.R
Saving _problems/test_node_lmer-178.R
Saving _problems/test_node_lmer-208.R
Saving _problems/test_node_lmer-239.R
Saving _problems/test_node_lmer-272.R
Saving _problems/test_node_lmer-393.R
Saving _problems/test_node_zeroinfl-114.R
t = 1 node = sickness2
t = 1 node = sickness1
t = 2 node = sickness2
t = 2 node = sickness1
t = 3 node = sickness2
t = 3 node = sickness1
t = 4 node = sickness2
t = 4 node = sickness1
t = 5 node = sickness2
t = 5 node = sickness1
starting worker pid=2786841 on localhost:11771 at 22:14:24.299
starting worker pid=2786840 on localhost:11771 at 22:14:24.405
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Loading required package: simDAG
loaded simDAG and set parent environment
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=2788106 on localhost:11771 at 22:14:28.904
starting worker pid=2788105 on localhost:11771 at 22:14:28.908
Loading required package: simDAG
Loading required package: simDAG
loaded simDAG and set parent environment
loaded simDAG and set parent environment
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Attaching package: ‘data.table’
Loading required package: foreach
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
Loading required package: rngtools
starting worker pid=2790604 on localhost:11771 at 22:14:36.087
starting worker pid=2790605 on localhost:11771 at 22:14:36.104
Loading required package: simDAG
Loading required package: simDAG
loaded simDAG and set parent environment
loaded simDAG and set parent environment
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: foreach
Loading required package: rngtools
Loading required package: rngtools
starting worker pid=2792619 on localhost:11771 at 22:14:43.428
starting worker pid=2792620 on localhost:11771 at 22:14:43.515
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Loading required package: simDAG
loaded simDAG and set parent environment
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’
The following object is masked from ‘package:base’:
%notin%
Loading required package: rngtools
Loading required package: foreach
Loading required package: rngtools
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|======================================================================| 100%starting worker pid=2794157 on localhost:11771 at 22:14:48.901
starting worker pid=2794156 on localhost:11771 at 22:14:48.911
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loaded simDAG and set parent environment
Loading required package: simDAG
Attaching package: ‘data.table’
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%notin%
Loading required package: foreach
Loading required package: rngtools
loaded simDAG and set parent environment
Attaching package: ‘data.table’
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%notin%
Loading required package: foreach
Loading required package: rngtools
|
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|======================================================================| 100%starting worker pid=2796903 on localhost:11771 at 22:14:52.994
starting worker pid=2796904 on localhost:11771 at 22:14:53.112
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| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
Loading required package: simDAG
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
loaded simDAG and set parent environment
Loading required package: rngtools
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
Loading required package: foreach
Loading required package: rngtools
|
|=================================== | 50%
|
|======================================================================| 100%[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ]
══ Skipped tests (56) ══════════════════════════════════════════════════════════
• On CRAN (56): 'test_DAG.network_S3.r:4:1', 'test_DAG.network_S3.r:10:1',
'test_DAG.network_S3.r:18:1', 'test_DAG.network_S3.r:24:1',
'test_DAG.network_S3.r:32:1', 'test_DAG.network_S3.r:44:1',
'test_DAG.network_S3.r:50:1', 'test_DAG.network_S3.r:58:1',
'test_DAG.network_S3.r:64:1', 'test_DAG.network_S3.r:72:1',
'test_DAG.node_S3.r:4:1', 'test_DAG.node_S3.r:9:1',
'test_DAG.node_S3.r:14:1', 'test_DAG.node_S3.r:19:1',
'test_DAG.node_S3.r:24:1', 'test_DAG.node_S3.r:32:1',
'test_DAG.node_S3.r:37:1', 'test_DAG.node_S3.r:42:1',
'test_DAG.node_S3.r:47:1', 'test_DAG.node_S3.r:52:1', 'test_dag.r:14:1',
'test_dag.r:21:1', 'test_dag.r:34:1', 'test_dag.r:44:1', 'test_dag.r:51:1',
'test_dag.r:64:1', 'test_node.r:548:1', 'test_node_rsurv.r:99:3',
'test_plot.DAG.r:11:1', 'test_plot.DAG.r:15:1', 'test_plot.DAG.r:19:1',
'test_plot.DAG.r:23:1', 'test_plot.DAG.r:27:1', 'test_plot.DAG.r:31:1',
'test_plot.DAG.r:35:1', 'test_plot.DAG.r:40:1', 'test_plot.DAG.r:44:1',
'test_plot.DAG.r:52:1', 'test_plot.DAG.r:59:1', 'test_plot.DAG.r:64:1',
'test_plot.DAG.r:69:1', 'test_plot.DAG.r:100:1', 'test_plot.DAG.r:104:1',
'test_plot.DAG.r:108:1', 'test_plot.simDT.r:24:1', 'test_plot.simDT.r:28:1',
'test_plot.simDT.r:32:1', 'test_plot.simDT.r:36:1', 'test_plot.simDT.r:40:1',
'test_plot.simDT.r:48:1', 'test_plot.simDT.r:56:1', 'test_simDT_S3.r:11:1',
'test_simDT_S3.r:15:1', 'test_simDT_S3.r:20:1', 'test_simDT_S3.r:25:1',
'test_sim_discrete_event.r:693:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_node_lmer.r:21:3'): simple random effect ───────────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:21:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:52:3'): simple random effect in disrete-time simulation ──
Error: An error occured when processing node 'Y' at time t = 1. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_discrete_time(...) at test_node_lmer.r:52:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:85:3'): simple random effect + categorical fixed effect ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:85:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:116:3'): simple random effect + interaction effect ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:116:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:148:3'): simple random effect + interaction effect of categorical vars ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:148:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:178:3'): simple random effect + cubic terms ────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:178:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:208:3'): simple random effect + ONLY cubic terms ───
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:208:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:239:3'): multiple random effects ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=2, npar=2, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:239:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:272:3'): with random effects and random slopes ─────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=3, npar=3, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:272:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:393:3'): simple random effect with non-default link ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:393:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_zeroinfl.r:114:3'): with random effects ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_zeroinfl.r:114:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
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=48060 on localhost:11936 at 13:49:32.634
starting worker pid=104512 on localhost:11936 at 13:49:32.655
|
| | 0%Loading required package: simDAG
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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%notin%
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|======================================================================| 100%starting worker pid=59140 on localhost:11936 at 13:49:35.192
starting worker pid=62380 on localhost:11936 at 13:49:35.194
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loaded simDAG and set parent environment
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The following object is masked from 'package:base':
%notin%
Loading required package: foreach
Loading required package: rngtools
Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Loading required package: foreach
Loading required package: rngtools
starting worker pid=68672 on localhost:11936 at 13:49:38.503
starting worker pid=40488 on localhost:11936 at 13:49:38.530
Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: 'data.table'
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%notin%
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Loading required package: rngtools
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loaded simDAG and set parent environment
Attaching package: 'data.table'
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%notin%
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Loading required package: rngtools
starting worker pid=112008 on localhost:11936 at 13:49:42.163
starting worker pid=20336 on localhost:11936 at 13:49:42.179
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: 'data.table'
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%notin%
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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%notin%
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|
|======= | 10%
|
|============== | 20%
|
|===================== | 30%
|
|============================ | 40%
|
|=================================== | 50%
|
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|
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|======================================================== | 80%
|
|=============================================================== | 90%
|
|======================================================================| 100%starting worker pid=77732 on localhost:11936 at 13:49:45.213
starting worker pid=86280 on localhost:11936 at 13:49:45.247
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: 'data.table'
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%notin%
Loading required package: foreach
Loading required package: rngtools
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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=74648 on localhost:11936 at 13:49:47.874
starting worker pid=11304 on localhost:11936 at 13:49:47.889
|
| | 0%Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Loading required package: foreach
Loading required package: rngtools
Loading required package: simDAG
loaded simDAG and set parent environment
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Loading required package: foreach
Loading required package: rngtools
|
|=================================== | 50%
|
|======================================================================| 100%[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ]
══ Skipped tests (56) ══════════════════════════════════════════════════════════
• On CRAN (56): 'test_DAG.network_S3.r:4:1', 'test_DAG.network_S3.r:10:1',
'test_DAG.network_S3.r:18:1', 'test_DAG.network_S3.r:24:1',
'test_DAG.network_S3.r:32:1', 'test_DAG.network_S3.r:44:1',
'test_DAG.network_S3.r:50:1', 'test_DAG.network_S3.r:58:1',
'test_DAG.network_S3.r:64:1', 'test_DAG.network_S3.r:72:1',
'test_DAG.node_S3.r:4:1', 'test_DAG.node_S3.r:9:1',
'test_DAG.node_S3.r:14:1', 'test_DAG.node_S3.r:19:1',
'test_DAG.node_S3.r:24:1', 'test_DAG.node_S3.r:32:1',
'test_DAG.node_S3.r:37:1', 'test_DAG.node_S3.r:42:1',
'test_DAG.node_S3.r:47:1', 'test_DAG.node_S3.r:52:1', 'test_dag.r:14:1',
'test_dag.r:21:1', 'test_dag.r:34:1', 'test_dag.r:44:1', 'test_dag.r:51:1',
'test_dag.r:64:1', 'test_node.r:548:1', 'test_node_rsurv.r:99:3',
'test_plot.DAG.r:11:1', 'test_plot.DAG.r:15:1', 'test_plot.DAG.r:19:1',
'test_plot.DAG.r:23:1', 'test_plot.DAG.r:27:1', 'test_plot.DAG.r:31:1',
'test_plot.DAG.r:35:1', 'test_plot.DAG.r:40:1', 'test_plot.DAG.r:44:1',
'test_plot.DAG.r:52:1', 'test_plot.DAG.r:59:1', 'test_plot.DAG.r:64:1',
'test_plot.DAG.r:69:1', 'test_plot.DAG.r:100:1', 'test_plot.DAG.r:104:1',
'test_plot.DAG.r:108:1', 'test_plot.simDT.r:24:1', 'test_plot.simDT.r:28:1',
'test_plot.simDT.r:32:1', 'test_plot.simDT.r:36:1', 'test_plot.simDT.r:40:1',
'test_plot.simDT.r:48:1', 'test_plot.simDT.r:56:1', 'test_simDT_S3.r:11:1',
'test_simDT_S3.r:15:1', 'test_simDT_S3.r:20:1', 'test_simDT_S3.r:25:1',
'test_sim_discrete_event.r:693:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_node_lmer.r:21:3'): simple random effect ───────────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:21:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:52:3'): simple random effect in disrete-time simulation ──
Error: An error occured when processing node 'Y' at time t = 1. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_discrete_time(...) at test_node_lmer.r:52:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:85:3'): simple random effect + categorical fixed effect ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:85:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:116:3'): simple random effect + interaction effect ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:116:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:148:3'): simple random effect + interaction effect of categorical vars ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:148:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:178:3'): simple random effect + cubic terms ────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:178:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:208:3'): simple random effect + ONLY cubic terms ───
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:208:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:239:3'): multiple random effects ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=2, npar=2, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:239:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:272:3'): with random effects and random slopes ─────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=3, npar=3, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:272:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_lmer.r:393:3'): simple random effect with non-default link ──
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag_bin, n_sim = 100) at test_node_lmer.r:393:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test_node_zeroinfl.r:114:3'): with random effects ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in mkMerMod(rho, opt, glmod$reTrms, fr = glmod$fr, mc = mcout, lme4conv = cc): unexpected parameter vector length: length(pars)=1, npar=1, nAGQ=1; (expected length(pars)==npar iff nAGQ==0)
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_zeroinfl.r:114:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
[ FAIL 11 | WARN 14 | SKIP 56 | PASS 1032 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-windows-x86_64
Version: 1.0.1
Check: tests
Result: ERROR
Running 'testthat.R' [127s]
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_network-108.R
Saving _problems/test_node_rsurv-11.R
Saving _problems/test_node_rsurv-24.R
Saving _problems/test_node_rsurv-37.R
Saving _problems/test_node_rsurv-50.R
Saving _problems/test_node_rsurv-63.R
Saving _problems/test_node_rsurv-76.R
Saving _problems/test_node_rsurv-90.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
Saving _problems/test_sim_from_dag-166.R
starting worker pid=35004 on localhost:11395 at 13:22:02.769
starting worker pid=31224 on localhost:11395 at 13:22:02.769
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loaded simDAG and set parent environment
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loaded simDAG and set parent environment
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loaded simDAG and set parent environment
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|
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starting worker pid=112220 on localhost:11395 at 13:22:19.362
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|======================================================================| 100%[ FAIL 9 | WARN 14 | SKIP 58 | PASS 1002 ]
══ Skipped tests (58) ══════════════════════════════════════════════════════════
• 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'
• Skipping (2): 'test_node_lmer.r:2:1', 'test_node_zeroinfl.r:101:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_network.r:108:3'): sorting with net() terms ────────────────────
Error in `inDL(x, as.logical(local), as.logical(now), ...)`: unable to load shared object 'D:/RCompile/CRANpkg/lib/4.5/Rfast/libs/x64/Rfast.dll':
LoadLibrary failure: Die angegebene Prozedur wurde nicht gefunden.
Backtrace:
▆
1. ├─simDAG::sim_from_dag(dag, n_sim = 10, sort_dag = TRUE) at test_network.r:108:3
2. └─base::loadNamespace(x)
3. └─base::library.dynam(lib, package, package.lib)
4. └─base::dyn.load(file, DLLpath = DLLpath, ...)
5. └─base (local) inDL(x, as.logical(local), as.logical(now), ...)
── Error ('test_node_rsurv.r:11:3'): general test case aftreg ──────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in inDL(x, as.logical(local), as.logical(now), ...): unable to load shared object 'D:/RCompile/CRANpkg/lib/4.5/rstan/libs/x64/rstan.dll':
LoadLibrary failure: Die angegebene Prozedur wurde nicht gefunden.
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_rsurv.r:11:3
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_rsurv.r:24:3'): general test case ahreg ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in inDL(x, as.logical(local), as.logical(now), ...): unable to load shared object 'D:/RCompile/CRANpkg/lib/4.5/rstan/libs/x64/rstan.dll':
LoadLibrary failure: Die angegebene Prozedur wurde nicht gefunden.
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_rsurv.r:24:3
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_rsurv.r:37:3'): general test case ehreg ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in inDL(x, as.logical(local), as.logical(now), ...): unable to load shared object 'D:/RCompile/CRANpkg/lib/4.5/rstan/libs/x64/rstan.dll':
LoadLibrary failure: Die angegebene Prozedur wurde nicht gefunden.
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_rsurv.r:37:3
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_rsurv.r:50:3'): general test case ypreg ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in inDL(x, as.logical(local), as.logical(now), ...): unable to load shared object 'D:/RCompile/CRANpkg/lib/4.5/rstan/libs/x64/rstan.dll':
LoadLibrary failure: Die angegebene Prozedur wurde nicht gefunden.
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_rsurv.r:50:3
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_rsurv.r:63:3'): general test case poreg ───────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in inDL(x, as.logical(local), as.logical(now), ...): unable to load shared object 'D:/RCompile/CRANpkg/lib/4.5/rstan/libs/x64/rstan.dll':
LoadLibrary failure: Die angegebene Prozedur wurde nicht gefunden.
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_rsurv.r:63:3
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_rsurv.r:76:3'): just as one column ────────────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in inDL(x, as.logical(local), as.logical(now), ...): unable to load shared object 'D:/RCompile/CRANpkg/lib/4.5/rstan/libs/x64/rstan.dll':
LoadLibrary failure: Die angegebene Prozedur wurde nicht gefunden.
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_rsurv.r:76:3
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_rsurv.r:90:3'): with censoring ────────────────────────────
Error: An error occured when processing node 'Y'. The message was:
Error in inDL(x, as.logical(local), as.logical(now), ...): unable to load shared object 'D:/RCompile/CRANpkg/lib/4.5/rstan/libs/x64/rstan.dll':
LoadLibrary failure: Die angegebene Prozedur wurde nicht gefunden.
Backtrace:
▆
1. └─simDAG::sim_from_dag(dag, n_sim = 100) at test_node_rsurv.r:90:3
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_sim_from_dag.r:166:5'): sort_dag working ───────────────────────
Error in `inDL(x, as.logical(local), as.logical(now), ...)`: unable to load shared object 'D:/RCompile/CRANpkg/lib/4.5/Rfast/libs/x64/Rfast.dll':
LoadLibrary failure: Die angegebene Prozedur wurde nicht gefunden.
Backtrace:
▆
1. ├─simDAG::sim_from_dag(n_sim = 20, dag = dag, sort_dag = TRUE) at test_sim_from_dag.r:166:5
2. └─base::loadNamespace(x)
3. └─base::library.dynam(lib, package, package.lib)
4. └─base::dyn.load(file, DLLpath = DLLpath, ...)
5. └─base (local) inDL(x, as.logical(local), as.logical(now), ...)
[ FAIL 9 | WARN 14 | SKIP 58 | PASS 1002 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64