Last updated on 2026-05-01 20:49:28 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.2.0 | 0.35 | 3.44 | 3.79 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.2.0 | 0.31 | 2.71 | 3.02 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.2.0 | 3.38 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.2.0 | 3.20 | ERROR | |||
| r-devel-windows-x86_64 | 2.2.0 | 29.00 | 98.00 | 127.00 | OK | |
| r-patched-linux-x86_64 | 2.2.0 | 0.28 | 2.15 | 2.43 | ERROR | |
| r-release-linux-x86_64 | 2.2.0 | 0.27 | 2.18 | 2.45 | ERROR | |
| r-release-macos-arm64 | 2.2.0 | OK | ||||
| r-release-macos-x86_64 | 2.2.0 | 47.00 | 571.00 | 618.00 | ERROR | |
| r-release-windows-x86_64 | 2.2.0 | 22.00 | 98.00 | 120.00 | OK | |
| r-oldrel-macos-arm64 | 2.2.0 | 3.00 | 30.00 | 33.00 | OK | |
| r-oldrel-macos-x86_64 | 2.2.0 | 10.00 | 94.00 | 104.00 | OK | |
| r-oldrel-windows-x86_64 | 2.2.0 | 26.00 | 117.00 | 143.00 | OK |
Version: 2.2.0
Check: package dependencies
Result: ERROR
Package required but not available: ‘TreeDist’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 2.2.0
Check: examples
Result: ERROR
Running examples in ‘Rogue-Ex.R’ failed
The error most likely occurred in:
> ### Name: RogueTaxa
> ### Title: Drop rogue taxa to generate a more informative consensus
> ### Aliases: RogueTaxa QuickRogue C_RogueNaRok
>
> ### ** Examples
>
> library("TreeTools", warn.conflicts = FALSE)
Loading required package: ape
>
> trees <- list(read.tree(text = ("(a, (b, (c, (d, (e, (X1, X2))))));")),
+ read.tree(text = ("((a, (X1, X2)), (b, (c, (d, e))));")))
> RogueTaxa(trees, dropsetSize = 2)
Error in consensus_info(trees, mode == 1L, p = safeP) :
object '_TreeDist_consensus_info' not found
Calls: RogueTaxa -> Roguehalla -> ConsensusInfo -> consensus_info
Execution halted
Flavor: r-release-macos-x86_64
Version: 2.2.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [20s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library("testthat")
> library("Rogue")
>
> test_check("Rogue")
Saving _problems/test-RogueTaxa-11.R
Saving _problems/test-RogueTaxa-50.R
Saving _problems/test-spic-4.R
Saving _problems/test-spic-29.R
Saving _problems/test-spic-59.R
Saving _problems/test-spic-105.R
[ FAIL 6 | WARN 0 | SKIP 0 | PASS 50 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-RogueTaxa.R:11:3'): RogueTaxa() handles bad input ──────────────
Error in `consensus_info(trees, mode == 1L, p = safeP)`: object '_TreeDist_consensus_info' not found
Backtrace:
▆
1. ├─testthat::expect_equal(RogueTaxa(c(bal8, bal8)), RogueTaxa(bal8)) at test-RogueTaxa.R:11:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─Rogue::RogueTaxa(c(bal8, bal8))
5. └─Rogue:::Roguehalla(...)
6. └─TreeDist::ConsensusInfo(trees, info = info, p = p, check.tips = FALSE)
7. └─TreeDist:::consensus_info(trees, mode == 1L, p = safeP)
── Error ('test-RogueTaxa.R:50:3'): Wilkinson & Crotti's examples are satisfied ──
Error in `consensus_info(trees, mode == 1L, p = safeP)`: object '_TreeDist_consensus_info' not found
Backtrace:
▆
1. ├─testthat::expect_equal("X", RogueTaxa(fig2)[2, "taxon"]) at test-RogueTaxa.R:50:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─Rogue::RogueTaxa(fig2)
5. └─Rogue:::Roguehalla(...)
6. └─TreeDist::ConsensusInfo(trees, info = info, p = p, check.tips = FALSE)
7. └─TreeDist:::consensus_info(trees, mode == 1L, p = safeP)
── Error ('test-spic.R:4:3'): Roguehalla() handles odd input ───────────────────
Error in `consensus_info(trees, mode == 1L, p = safeP)`: object '_TreeDist_consensus_info' not found
Backtrace:
▆
1. └─TreeDist::ConsensusInfo(...) at test-spic.R:4:3
2. └─TreeDist:::consensus_info(trees, mode == 1L, p = safeP)
── Error ('test-spic.R:29:3'): QuickRogue() ────────────────────────────────────
Error in `consensus_info(trees, mode == 1L, p = safeP)`: object '_TreeDist_consensus_info' not found
Backtrace:
▆
1. ├─testthat::expect_equal(2L, nrow(QuickRogue(trees))) at test-spic.R:29:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(QuickRogue(trees))
5. └─Rogue::QuickRogue(trees)
6. └─TreeDist::ConsensusInfo(trees, info = info, p = p, check.tips = FALSE)
7. └─TreeDist:::consensus_info(trees, mode == 1L, p = safeP)
── Error ('test-spic.R:59:3'): Rogues found ────────────────────────────────────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_shared_phylo' not found
Backtrace:
▆
1. └─Rogue::TipVolatility(trees) at test-spic.R:59:3
2. └─base::vapply(...)
3. └─Rogue (local) FUN(X[[i]], ...)
4. ├─base::mean(PhylogeneticInfoDistance(tr, normalize = TRUE))
5. └─TreeDist::PhylogeneticInfoDistance(tr, normalize = TRUE)
6. └─TreeDist::SharedPhylogeneticInfo(...)
7. └─TreeDist::CalculateTreeDistance(...)
8. └─TreeDist:::.SplitDistanceAllPairs(...)
9. ├─base::structure(...)
10. └─base::apply(is, 2, .CliPairDist)
11. └─TreeDist (local) FUN(newX[, i], ...)
12. └─TreeDist (local) .PairDist(i)
13. └─TreeDist (local) Func(...)
14. └─TreeDist::GeneralizedRF(...)
15. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
── Error ('test-spic.R:105:3'): QuickRogue() restores leaves ───────────────────
Error in `consensus_info(trees, mode == 1L, p = safeP)`: object '_TreeDist_consensus_info' not found
Backtrace:
▆
1. ├─testthat::expect_equal(nrow(QuickRogue(trees150[80:89])), 5) at test-spic.R:105:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::nrow(QuickRogue(trees150[80:89]))
5. └─Rogue::QuickRogue(trees150[80:89])
6. └─TreeDist::ConsensusInfo(trees, info = info, p = p, check.tips = FALSE)
7. └─TreeDist:::consensus_info(trees, mode == 1L, p = safeP)
[ FAIL 6 | WARN 0 | SKIP 0 | PASS 50 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-macos-x86_64
Version: 2.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Bayesian.Rmd’ using rmarkdown
Quitting from Bayesian.Rmd:146-153 [find-rogues]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `consensus_info()`:
! object '_TreeDist_consensus_info' not found
---
Backtrace:
▆
1. └─Rogue::QuickRogue(trees)
2. └─TreeDist::ConsensusInfo(trees, info = info, p = p, check.tips = FALSE)
3. └─TreeDist:::consensus_info(trees, mode == 1L, p = safeP)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Bayesian.Rmd' failed with diagnostics:
object '_TreeDist_consensus_info' not found
--- failed re-building ‘Bayesian.Rmd’
SUMMARY: processing the following file failed:
‘Bayesian.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64