Last updated on 2025-12-25 15:54:11 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.0 | 572.93 | 370.94 | 943.87 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.1.0 | 354.02 | 256.88 | 610.90 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.1.0 | 1380.00 | 744.69 | 2124.69 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.1.0 | 1140.00 | 683.06 | 1823.06 | OK | |
| r-devel-windows-x86_64 | 2.1.0 | 650.00 | 523.00 | 1173.00 | OK | |
| r-patched-linux-x86_64 | 2.1.0 | 532.52 | 449.05 | 981.57 | OK | |
| r-release-linux-x86_64 | 2.1.0 | 508.50 | 439.94 | 948.44 | OK | |
| r-release-macos-arm64 | 2.1.0 | OK | ||||
| r-release-macos-x86_64 | 2.1.0 | 329.00 | 159.00 | 488.00 | OK | |
| r-release-windows-x86_64 | 2.1.0 | 665.00 | 517.00 | 1182.00 | OK | |
| r-oldrel-macos-arm64 | 2.1.0 | NOTE | ||||
| r-oldrel-macos-x86_64 | 2.1.0 | 329.00 | 189.00 | 518.00 | NOTE | |
| r-oldrel-windows-x86_64 | 2.1.0 | 775.00 | 643.00 | 1418.00 | OK |
Version: 2.1.0
Check: examples
Result: ERROR
Running examples in ‘seqHMM-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build_lcm
> ### Title: Build a Latent Class Model
> ### Aliases: build_lcm
>
> ### ** Examples
>
> # Simulate observations from two classes
> set.seed(123)
> obs <- seqdef(rbind(
+ matrix(sample(letters[1:3], 500, TRUE, prob = c(0.1, 0.6, 0.3)), 50, 10),
+ matrix(sample(letters[1:3], 200, TRUE, prob = c(0.4, 0.4, 0.2)), 20, 10)
+ ))
[>] 3 distinct states appear in the data:
1 = a
2 = b
3 = c
[>] state coding:
[alphabet] [label] [long label]
1 a a a
2 b b b
3 c c c
[>] 70 sequences in the data set
[>] min/max sequence length: 10/10
>
> # Initialize the model
> set.seed(9087)
> model <- build_lcm(obs, n_clusters = 2)
>
> # Estimate model parameters
> fit <- fit_model(model)
>
> # How many of the observations were correctly classified:
> sum(summary(fit$model)$most_probable_cluster == rep(c("Class 2", "Class 1"),
+ times = c(500, 200)))
Error in `[.data.table`(out, , `:=`(ll, logSumExp(log_alpha[time == time[.N]])), :
attempt access index 6/6 in VECTOR_ELT
Calls: summary ... posterior_probs -> posterior_probs.mhmm -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [92s/78s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(seqHMM)
Please cite seqHMM appropriately, see `citation('seqHMM')` for details.
>
> test_check("seqHMM")
Saving _problems/test-bootstrap-63.R
Saving _problems/test-bootstrap-67.R
Saving _problems/test-bootstrap-68.R
Saving _problems/test-bootstrap-123.R
Saving _problems/test-bootstrap-124.R
Saving _problems/test-bootstrap-125.R
Saving _problems/test-formulas-62.R
Saving _problems/test-formulas-66.R
Saving _problems/test-formulas-67.R
Saving _problems/test-get_probs-42.R
Saving _problems/test-get_probs-122.R
Saving _problems/test-get_probs-142.R
Saving _problems/test-get_probs-200.R
Saving _problems/test-get_probs-204.R
Saving _problems/test-misc-117.R
Saving _problems/test-posterior_probs-7.R
Saving _problems/test-posterior_probs-8.R
Saving _problems/test-posterior_probs-16.R
Saving _problems/test-posterior_probs-17.R
Saving _problems/test-posterior_probs-38.R
Saving _problems/test-posterior_probs-39.R
Saving _problems/test-posterior_probs-78.R
Saving _problems/test-posterior_probs-79.R
Saving _problems/test-predict-66.R
[ FAIL 24 | WARN 0 | SKIP 2 | PASS 302 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• run_extended_tests is not TRUE (2): 'test-extended.R:5:5',
'test-extended.R:88:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-bootstrap.R:60:3'): boostrap works for `mnhmm` ───────────────
Expected `fit <- bootstrap_coefs(fit, type = "nonparametric", nsim = 2)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-bootstrap.R:60:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::bootstrap_coefs(fit, type = "nonparametric", nsim = 2)
8. └─seqHMM:::bootstrap_coefs.mnhmm(fit, type = "nonparametric", nsim = 2)
9. ├─base::matrix(...)
10. └─seqHMM::posterior_cluster_probabilities(model)
11. ├─seqHMM::posterior_probs(x)
12. └─seqHMM:::posterior_probs.mnhmm(x)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Failure ('test-bootstrap.R:64:3'): boostrap works for `mnhmm` ───────────────
Expected `fit <- bootstrap_coefs(fit, type = "parametric", nsim = 2, append = TRUE)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-bootstrap.R:64:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::bootstrap_coefs(fit, type = "parametric", nsim = 2, append = TRUE)
8. └─seqHMM:::bootstrap_coefs.mnhmm(...)
9. ├─base::matrix(...)
10. └─seqHMM::posterior_cluster_probabilities(model)
11. ├─seqHMM::posterior_probs(x)
12. └─seqHMM:::posterior_probs.mnhmm(x)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Failure ('test-bootstrap.R:68:3'): boostrap works for `mnhmm` ───────────────
Expected `length(fit$boot)` to equal 5L.
Differences:
`actual`: 0
`expected`: 5
── Failure ('test-bootstrap.R:120:3'): boostrap works for `mfanhmm` ────────────
Expected `fit <- bootstrap_coefs(fit, type = "nonparametric", nsim = 2)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-bootstrap.R:120:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::bootstrap_coefs(fit, type = "nonparametric", nsim = 2)
8. └─seqHMM:::bootstrap_coefs.mnhmm(fit, type = "nonparametric", nsim = 2)
9. ├─base::matrix(...)
10. └─seqHMM::posterior_cluster_probabilities(model)
11. ├─seqHMM::posterior_probs(x)
12. └─seqHMM:::posterior_probs.mnhmm(x)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Failure ('test-bootstrap.R:124:3'): boostrap works for `mfanhmm` ────────────
Expected `length(fit$boot)` to equal 5L.
Differences:
`actual`: 0
`expected`: 5
── Failure ('test-bootstrap.R:125:3'): boostrap works for `mfanhmm` ────────────
Expected `length(fit$boot[[1]])` to equal 2L.
Differences:
`actual`: 0
`expected`: 2
── Failure ('test-formulas.R:59:3'): boostrap works for `mnhmm` ────────────────
Expected `fit <- bootstrap_coefs(fit, type = "nonparametric", nsim = 2)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-formulas.R:59:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::bootstrap_coefs(fit, type = "nonparametric", nsim = 2)
8. └─seqHMM:::bootstrap_coefs.mnhmm(fit, type = "nonparametric", nsim = 2)
9. ├─base::matrix(...)
10. └─seqHMM::posterior_cluster_probabilities(model)
11. ├─seqHMM::posterior_probs(x)
12. └─seqHMM:::posterior_probs.mnhmm(x)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Failure ('test-formulas.R:63:3'): boostrap works for `mnhmm` ────────────────
Expected `fit <- bootstrap_coefs(fit, type = "parametric", nsim = 2, append = TRUE)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-formulas.R:63:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::bootstrap_coefs(fit, type = "parametric", nsim = 2, append = TRUE)
8. └─seqHMM:::bootstrap_coefs.mnhmm(...)
9. ├─base::matrix(...)
10. └─seqHMM::posterior_cluster_probabilities(model)
11. ├─seqHMM::posterior_probs(x)
12. └─seqHMM:::posterior_probs.mnhmm(x)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Failure ('test-formulas.R:67:3'): boostrap works for `mnhmm` ────────────────
Expected `length(fit$boot)` to equal 5L.
Differences:
`actual`: 0
`expected`: 5
── Failure ('test-get_probs.R:39:3'): 'get_probs' and 'coef' works for multichannel 'nhmm' ──
Expected `marginals <- get_marginals(fit)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(marginals <- get_marginals(fit), NA) at test-get_probs.R:39:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─seqHMM::get_marginals(fit)
8. ├─seqHMM::posterior_probs(model)
9. └─seqHMM:::posterior_probs.nhmm(model)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Failure ('test-get_probs.R:119:3'): 'get_probs' and 'coef' works for single-channel 'mnhmm' ──
Expected `fit <- bootstrap_coefs(fit, nsim = 10)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-get_probs.R:119:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::bootstrap_coefs(fit, nsim = 10)
8. └─seqHMM:::bootstrap_coefs.mnhmm(fit, nsim = 10)
9. ├─base::matrix(...)
10. └─seqHMM::posterior_cluster_probabilities(model)
11. ├─seqHMM::posterior_probs(x)
12. └─seqHMM:::posterior_probs.mnhmm(x)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Failure ('test-get_probs.R:139:3'): 'get_probs' and 'coef' works for single-channel 'mnhmm' ──
Expected `coef(fit, probs = 0.5)` not to throw any errors.
Actually got a <rlang_error> with message:
Model does not contain bootstrap samples of coefficients. Run `bootstrap_coefs()` first.
Backtrace:
▆
1. ├─testthat::expect_error(coef(fit, probs = 0.5), NA) at test-get_probs.R:139:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─stats::coef(fit, probs = 0.5)
8. └─seqHMM:::coef.mnhmm(fit, probs = 0.5)
9. └─seqHMM:::stopifnot_(...)
10. └─cli::cli_abort(message, ..., .envir = parent.frame(), call = call)
11. └─rlang::abort(...)
── Failure ('test-get_probs.R:197:3'): 'get_probs' and 'coef' works for 'fanhmm' ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-get_probs.R:197:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─seqHMM::get_marginals(fanhmm_leaves, probs = c(0.1, 0.5, 0.9))
8. ├─seqHMM::posterior_probs(model)
9. └─seqHMM:::posterior_probs.nhmm(model)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-get_probs.R:201:3'): 'get_probs' and 'coef' works for 'fanhmm' ──
Error in `eval(code, test_env)`: object 'marginals' not found
Backtrace:
▆
1. └─testthat::expect_equal(...) at test-get_probs.R:201:3
2. └─testthat::quasi_label(enquo(object), label)
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Error ('test-misc.R:114:3'): 'most_probable_cluster' works ──────────────────
Error in ``[.data.table`(out, , `:=`(ll, logSumExp(log_alpha[time == time[.N]])), by = id, showProgress = FALSE)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-misc.R:114:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─seqHMM::most_probable_cluster(mhmm_biofam, type = "posterior")
5. └─seqHMM::posterior_cluster_probabilities(x)
6. ├─seqHMM::posterior_probs(x)
7. └─seqHMM:::posterior_probs.mhmm(x)
8. ├─...[]
9. └─data.table:::`[.data.table`(...)
── Failure ('test-posterior_probs.R:4:3'): 'posterior_probs' works for 'hmm' ───
Expected `out <- posterior_probs(hmm_biofam)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(out <- posterior_probs(hmm_biofam), NA) at test-posterior_probs.R:4:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::posterior_probs(hmm_biofam)
8. └─seqHMM:::posterior_probs.hmm(hmm_biofam)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-posterior_probs.R:8:3'): 'posterior_probs' works for 'hmm' ─────
Error in `eval(code, test_env)`: object 'out' not found
Backtrace:
▆
1. └─testthat::expect_gte(min(out$probability), 0 - 1e-12) at test-posterior_probs.R:8:3
2. └─testthat::quasi_label(enquo(object), label)
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test-posterior_probs.R:13:3'): 'posterior_probs' works for 'mhmm' ──
Expected `out <- posterior_probs(mhmm_biofam)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(out <- posterior_probs(mhmm_biofam), NA) at test-posterior_probs.R:13:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::posterior_probs(mhmm_biofam)
8. └─seqHMM:::posterior_probs.mhmm(mhmm_biofam)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-posterior_probs.R:17:3'): 'posterior_probs' works for 'mhmm' ───
Error in `eval(code, test_env)`: object 'out' not found
Backtrace:
▆
1. └─testthat::expect_gte(min(out$probability), 0 - 1e-12) at test-posterior_probs.R:17:3
2. └─testthat::quasi_label(enquo(object), label)
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test-posterior_probs.R:35:3'): 'posterior_probs' works for 'nhmm' ──
Expected `out <- posterior_probs(fit)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(out <- posterior_probs(fit), NA) at test-posterior_probs.R:35:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::posterior_probs(fit)
8. └─seqHMM:::posterior_probs.nhmm(fit)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-posterior_probs.R:39:3'): 'posterior_probs' works for 'nhmm' ───
Error in `eval(code, test_env)`: object 'out' not found
Backtrace:
▆
1. └─testthat::expect_gte(min(out$probability), 0 - 1e-12) at test-posterior_probs.R:39:3
2. └─testthat::quasi_label(enquo(object), label)
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test-posterior_probs.R:75:3'): 'posterior_probs' works for 'mnhmm' ──
Expected `out <- posterior_probs(fit)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(out <- posterior_probs(fit), NA) at test-posterior_probs.R:75:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::posterior_probs(fit)
8. └─seqHMM:::posterior_probs.mnhmm(fit)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-posterior_probs.R:79:3'): 'posterior_probs' works for 'mnhmm' ──
Error in `eval(code, test_env)`: object 'out' not found
Backtrace:
▆
1. └─testthat::expect_gte(min(out$probability), 0 - 1e-12) at test-posterior_probs.R:79:3
2. └─testthat::quasi_label(enquo(object), label)
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Error ('test-predict.R:66:3'): 'predict' works 'mnhmm' ──────────────────────
Error in ``[.data.table`(out, , `:=`(ll, logSumExp(log_alpha[time_var == time_var[.N]])), by = id_var, env = list(id_var = id_var, time_var = time_var), showProgress = FALSE)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─seqHMM::bootstrap_coefs(fit, nsim = 5) at test-predict.R:66:3
2. └─seqHMM:::bootstrap_coefs.mnhmm(fit, nsim = 5)
3. ├─base::matrix(...)
4. └─seqHMM::posterior_cluster_probabilities(model)
5. ├─seqHMM::posterior_probs(x)
6. └─seqHMM:::posterior_probs.mnhmm(x)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
[ FAIL 24 | WARN 0 | SKIP 2 | PASS 302 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘seqHMM.Rnw’ using knitr
Quitting from seqHMM.Rnw:764-766 [code_summaryMHMM]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 6/6 in VECTOR_ELT
---
Backtrace:
x
1. +-base::summary(mhmm, conditional_se = FALSE)
2. \-seqHMM:::summary.mhmm(mhmm, conditional_se = FALSE)
3. \-seqHMM::posterior_cluster_probabilities(object)
4. +-seqHMM::posterior_probs(x)
5. \-seqHMM:::posterior_probs.mhmm(x)
6. +-...[]
7. \-data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'seqHMM.Rnw' failed with diagnostics:
attempt access index 6/6 in VECTOR_ELT
--- failed re-building ‘seqHMM.Rnw’
--- re-building ‘seqHMM_algorithms.Rnw’ using knitr
--- finished re-building ‘seqHMM_algorithms.Rnw’
--- re-building ‘seqHMM_estimation.Rnw’ using knitr
--- finished re-building ‘seqHMM_estimation.Rnw’
--- re-building ‘seqHMM_visualization.Rnw’ using knitr
--- finished re-building ‘seqHMM_visualization.Rnw’
SUMMARY: processing the following file failed:
‘seqHMM.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [66s/71s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(seqHMM)
Please cite seqHMM appropriately, see `citation('seqHMM')` for details.
>
> test_check("seqHMM")
Saving _problems/test-bootstrap-63.R
Saving _problems/test-bootstrap-67.R
Saving _problems/test-bootstrap-68.R
Saving _problems/test-bootstrap-123.R
Saving _problems/test-bootstrap-124.R
Saving _problems/test-bootstrap-125.R
Saving _problems/test-formulas-62.R
Saving _problems/test-formulas-66.R
Saving _problems/test-formulas-67.R
Saving _problems/test-get_probs-42.R
Saving _problems/test-get_probs-122.R
Saving _problems/test-get_probs-142.R
Saving _problems/test-get_probs-200.R
Saving _problems/test-get_probs-204.R
Saving _problems/test-misc-117.R
Saving _problems/test-posterior_probs-7.R
Saving _problems/test-posterior_probs-8.R
Saving _problems/test-posterior_probs-16.R
Saving _problems/test-posterior_probs-17.R
Saving _problems/test-posterior_probs-38.R
Saving _problems/test-posterior_probs-39.R
Saving _problems/test-posterior_probs-78.R
Saving _problems/test-posterior_probs-79.R
Saving _problems/test-predict-66.R
[ FAIL 24 | WARN 0 | SKIP 2 | PASS 302 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• run_extended_tests is not TRUE (2): 'test-extended.R:5:5',
'test-extended.R:88:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-bootstrap.R:60:3'): boostrap works for `mnhmm` ───────────────
Expected `fit <- bootstrap_coefs(fit, type = "nonparametric", nsim = 2)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-bootstrap.R:60:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::bootstrap_coefs(fit, type = "nonparametric", nsim = 2)
8. └─seqHMM:::bootstrap_coefs.mnhmm(fit, type = "nonparametric", nsim = 2)
9. ├─base::matrix(...)
10. └─seqHMM::posterior_cluster_probabilities(model)
11. ├─seqHMM::posterior_probs(x)
12. └─seqHMM:::posterior_probs.mnhmm(x)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Failure ('test-bootstrap.R:64:3'): boostrap works for `mnhmm` ───────────────
Expected `fit <- bootstrap_coefs(fit, type = "parametric", nsim = 2, append = TRUE)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-bootstrap.R:64:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::bootstrap_coefs(fit, type = "parametric", nsim = 2, append = TRUE)
8. └─seqHMM:::bootstrap_coefs.mnhmm(...)
9. ├─base::matrix(...)
10. └─seqHMM::posterior_cluster_probabilities(model)
11. ├─seqHMM::posterior_probs(x)
12. └─seqHMM:::posterior_probs.mnhmm(x)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Failure ('test-bootstrap.R:68:3'): boostrap works for `mnhmm` ───────────────
Expected `length(fit$boot)` to equal 5L.
Differences:
`actual`: 0
`expected`: 5
── Failure ('test-bootstrap.R:120:3'): boostrap works for `mfanhmm` ────────────
Expected `fit <- bootstrap_coefs(fit, type = "nonparametric", nsim = 2)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-bootstrap.R:120:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::bootstrap_coefs(fit, type = "nonparametric", nsim = 2)
8. └─seqHMM:::bootstrap_coefs.mnhmm(fit, type = "nonparametric", nsim = 2)
9. ├─base::matrix(...)
10. └─seqHMM::posterior_cluster_probabilities(model)
11. ├─seqHMM::posterior_probs(x)
12. └─seqHMM:::posterior_probs.mnhmm(x)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Failure ('test-bootstrap.R:124:3'): boostrap works for `mfanhmm` ────────────
Expected `length(fit$boot)` to equal 5L.
Differences:
`actual`: 0
`expected`: 5
── Failure ('test-bootstrap.R:125:3'): boostrap works for `mfanhmm` ────────────
Expected `length(fit$boot[[1]])` to equal 2L.
Differences:
`actual`: 0
`expected`: 2
── Failure ('test-formulas.R:59:3'): boostrap works for `mnhmm` ────────────────
Expected `fit <- bootstrap_coefs(fit, type = "nonparametric", nsim = 2)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-formulas.R:59:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::bootstrap_coefs(fit, type = "nonparametric", nsim = 2)
8. └─seqHMM:::bootstrap_coefs.mnhmm(fit, type = "nonparametric", nsim = 2)
9. ├─base::matrix(...)
10. └─seqHMM::posterior_cluster_probabilities(model)
11. ├─seqHMM::posterior_probs(x)
12. └─seqHMM:::posterior_probs.mnhmm(x)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Failure ('test-formulas.R:63:3'): boostrap works for `mnhmm` ────────────────
Expected `fit <- bootstrap_coefs(fit, type = "parametric", nsim = 2, append = TRUE)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-formulas.R:63:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::bootstrap_coefs(fit, type = "parametric", nsim = 2, append = TRUE)
8. └─seqHMM:::bootstrap_coefs.mnhmm(...)
9. ├─base::matrix(...)
10. └─seqHMM::posterior_cluster_probabilities(model)
11. ├─seqHMM::posterior_probs(x)
12. └─seqHMM:::posterior_probs.mnhmm(x)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Failure ('test-formulas.R:67:3'): boostrap works for `mnhmm` ────────────────
Expected `length(fit$boot)` to equal 5L.
Differences:
`actual`: 0
`expected`: 5
── Failure ('test-get_probs.R:39:3'): 'get_probs' and 'coef' works for multichannel 'nhmm' ──
Expected `marginals <- get_marginals(fit)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(marginals <- get_marginals(fit), NA) at test-get_probs.R:39:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─seqHMM::get_marginals(fit)
8. ├─seqHMM::posterior_probs(model)
9. └─seqHMM:::posterior_probs.nhmm(model)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Failure ('test-get_probs.R:119:3'): 'get_probs' and 'coef' works for single-channel 'mnhmm' ──
Expected `fit <- bootstrap_coefs(fit, nsim = 10)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-get_probs.R:119:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::bootstrap_coefs(fit, nsim = 10)
8. └─seqHMM:::bootstrap_coefs.mnhmm(fit, nsim = 10)
9. ├─base::matrix(...)
10. └─seqHMM::posterior_cluster_probabilities(model)
11. ├─seqHMM::posterior_probs(x)
12. └─seqHMM:::posterior_probs.mnhmm(x)
13. ├─...[]
14. └─data.table:::`[.data.table`(...)
── Failure ('test-get_probs.R:139:3'): 'get_probs' and 'coef' works for single-channel 'mnhmm' ──
Expected `coef(fit, probs = 0.5)` not to throw any errors.
Actually got a <rlang_error> with message:
Model does not contain bootstrap samples of coefficients. Run `bootstrap_coefs()` first.
Backtrace:
▆
1. ├─testthat::expect_error(coef(fit, probs = 0.5), NA) at test-get_probs.R:139:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─stats::coef(fit, probs = 0.5)
8. └─seqHMM:::coef.mnhmm(fit, probs = 0.5)
9. └─seqHMM:::stopifnot_(...)
10. └─cli::cli_abort(message, ..., .envir = parent.frame(), call = call)
11. └─rlang::abort(...)
── Failure ('test-get_probs.R:197:3'): 'get_probs' and 'coef' works for 'fanhmm' ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-get_probs.R:197:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─seqHMM::get_marginals(fanhmm_leaves, probs = c(0.1, 0.5, 0.9))
8. ├─seqHMM::posterior_probs(model)
9. └─seqHMM:::posterior_probs.nhmm(model)
10. ├─...[]
11. └─data.table:::`[.data.table`(...)
── Error ('test-get_probs.R:201:3'): 'get_probs' and 'coef' works for 'fanhmm' ──
Error in `eval(code, test_env)`: object 'marginals' not found
Backtrace:
▆
1. └─testthat::expect_equal(...) at test-get_probs.R:201:3
2. └─testthat::quasi_label(enquo(object), label)
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Error ('test-misc.R:114:3'): 'most_probable_cluster' works ──────────────────
Error in ``[.data.table`(out, , `:=`(ll, logSumExp(log_alpha[time == time[.N]])), by = id, showProgress = FALSE)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-misc.R:114:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─seqHMM::most_probable_cluster(mhmm_biofam, type = "posterior")
5. └─seqHMM::posterior_cluster_probabilities(x)
6. ├─seqHMM::posterior_probs(x)
7. └─seqHMM:::posterior_probs.mhmm(x)
8. ├─...[]
9. └─data.table:::`[.data.table`(...)
── Failure ('test-posterior_probs.R:4:3'): 'posterior_probs' works for 'hmm' ───
Expected `out <- posterior_probs(hmm_biofam)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(out <- posterior_probs(hmm_biofam), NA) at test-posterior_probs.R:4:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::posterior_probs(hmm_biofam)
8. └─seqHMM:::posterior_probs.hmm(hmm_biofam)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-posterior_probs.R:8:3'): 'posterior_probs' works for 'hmm' ─────
Error in `eval(code, test_env)`: object 'out' not found
Backtrace:
▆
1. └─testthat::expect_gte(min(out$probability), 0 - 1e-12) at test-posterior_probs.R:8:3
2. └─testthat::quasi_label(enquo(object), label)
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test-posterior_probs.R:13:3'): 'posterior_probs' works for 'mhmm' ──
Expected `out <- posterior_probs(mhmm_biofam)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(out <- posterior_probs(mhmm_biofam), NA) at test-posterior_probs.R:13:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::posterior_probs(mhmm_biofam)
8. └─seqHMM:::posterior_probs.mhmm(mhmm_biofam)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-posterior_probs.R:17:3'): 'posterior_probs' works for 'mhmm' ───
Error in `eval(code, test_env)`: object 'out' not found
Backtrace:
▆
1. └─testthat::expect_gte(min(out$probability), 0 - 1e-12) at test-posterior_probs.R:17:3
2. └─testthat::quasi_label(enquo(object), label)
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test-posterior_probs.R:35:3'): 'posterior_probs' works for 'nhmm' ──
Expected `out <- posterior_probs(fit)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(out <- posterior_probs(fit), NA) at test-posterior_probs.R:35:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::posterior_probs(fit)
8. └─seqHMM:::posterior_probs.nhmm(fit)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-posterior_probs.R:39:3'): 'posterior_probs' works for 'nhmm' ───
Error in `eval(code, test_env)`: object 'out' not found
Backtrace:
▆
1. └─testthat::expect_gte(min(out$probability), 0 - 1e-12) at test-posterior_probs.R:39:3
2. └─testthat::quasi_label(enquo(object), label)
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test-posterior_probs.R:75:3'): 'posterior_probs' works for 'mnhmm' ──
Expected `out <- posterior_probs(fit)` not to throw any errors.
Actually got a <simpleError> with message:
attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_error(out <- posterior_probs(fit), NA) at test-posterior_probs.R:75:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─seqHMM::posterior_probs(fit)
8. └─seqHMM:::posterior_probs.mnhmm(fit)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
── Error ('test-posterior_probs.R:79:3'): 'posterior_probs' works for 'mnhmm' ──
Error in `eval(code, test_env)`: object 'out' not found
Backtrace:
▆
1. └─testthat::expect_gte(min(out$probability), 0 - 1e-12) at test-posterior_probs.R:79:3
2. └─testthat::quasi_label(enquo(object), label)
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Error ('test-predict.R:66:3'): 'predict' works 'mnhmm' ──────────────────────
Error in ``[.data.table`(out, , `:=`(ll, logSumExp(log_alpha[time_var == time_var[.N]])), by = id_var, env = list(id_var = id_var, time_var = time_var), showProgress = FALSE)`: attempt access index 6/6 in VECTOR_ELT
Backtrace:
▆
1. ├─seqHMM::bootstrap_coefs(fit, nsim = 5) at test-predict.R:66:3
2. └─seqHMM:::bootstrap_coefs.mnhmm(fit, nsim = 5)
3. ├─base::matrix(...)
4. └─seqHMM::posterior_cluster_probabilities(model)
5. ├─seqHMM::posterior_probs(x)
6. └─seqHMM:::posterior_probs.mnhmm(x)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
[ FAIL 24 | WARN 0 | SKIP 2 | PASS 302 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.0
Check: installed package size
Result: NOTE
installed size is 25.6Mb
sub-directories of 1Mb or more:
libs 23.3Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.