Last updated on 2025-12-20 17:50:41 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.0 | 572.23 | 368.69 | 940.92 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.1.0 | 359.41 | 249.69 | 609.10 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.1.0 | 1263.00 | 365.11 | 1628.11 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 2.1.0 | 1020.00 | 418.22 | 1438.22 | ERROR | |
| r-devel-windows-x86_64 | 2.1.0 | 650.00 | 523.00 | 1173.00 | OK | |
| r-patched-linux-x86_64 | 2.1.0 | 528.41 | 451.84 | 980.25 | 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 | 624.00 | 503.00 | 1127.00 | 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 | 773.00 | 626.00 | 1399.00 | 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’ [95s/75s]
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’ [58s/56s]
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: examples
Result: ERROR
Running examples in ‘seqHMM-Ex.R’ failed
The error most likely occurred in:
> ### 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-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 2.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [78s/60s]
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
OMP: Warning #96: Cannot form a team with 8 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
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-fedora-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
OMP: Warning #96: Cannot form a team with 8 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [61s/60s]
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-fedora-gcc
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
Flavor: r-devel-linux-x86_64-fedora-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