Last updated on 2026-05-26 13:55:24 CEST.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| CongreveLamsdell2016 | 13 | |||
| ips | 13 | |||
| motmot | 13 | |||
| PlotTools | 13 | |||
| Quartet | 13 | |||
| Rogue | 1 | 2 | 10 | |
| TBRDist | 13 | |||
| Ternary | 1 | 12 | ||
| TotalCopheneticIndex | 2 | 11 | ||
| TreeDist | 13 | |||
| TreeSearch | 1 | 12 | ||
| TreeTools | 1 | 12 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, NOTE: 2, OK: 10
Version: 2.2.0
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘matrixStats’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
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
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 2.3.6
Check: examples
Result: ERROR
Running examples in ‘Ternary-Ex.R’ failed
The error most likely occurred in:
> ### Name: Annotate
> ### Title: Annotate points on a ternary plot
> ### Aliases: Annotate
>
> ### ** Examples
>
> # Load some data
> data("Seatbelts")
> seats <- c("drivers", "front", "rear")
> seat <- Seatbelts[month.abb %in% "Oct", seats]
> law <- Seatbelts[month.abb %in% "Oct", "law"]
>
> # Set up plot
> oPar <- par(mar = c(2, 0, 0, 0))
> TernaryPlot(alab = seats[1], blab = seats[2], clab = seats[3])
> TernaryPoints(seat, cex = 0.8, col = 2 + law)
>
> # Annotate points by year
> Annotate(seat, labels = 1969:1984, col = 2 + law)
Error in lapjv(x, max(x)) : object '_TreeDist_lapjv' not found
Calls: Annotate -> LAPJV -> lapjv
Execution halted
Flavor: r-release-macos-x86_64
Version: 2.3.6
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [17s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library("testthat")
> library("Ternary")
>
> test_check("Ternary")
Saving _problems/test-Annotate-12.R
[ FAIL 1 | WARN 1 | SKIP 10 | PASS 117 ]
══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-Contours.R:22:1', 'test-Contours.R:234:1',
'test-Contours.R:243:1', 'test-Holdridge.R:8:1', 'test-axis-rotate.R:1:1',
'test-axis-rotate.R:69:1', 'test-ternary.R:46:1', 'test-ternary.R:70:1',
'test-ternary.R:130:1', 'test-ternary.R:142:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-Annotate.R:12:5'): Annotate() works ────────────────────────────
Error in `lapjv(x, max(x))`: object '_TreeDist_lapjv' not found
Backtrace:
▆
1. └─vdiffr::expect_doppelganger("Annotate-basics", AnnotateBasics) at test-Annotate.R:20:3
2. └─vdiffr (local) writer(fig, testcase, title)
3. ├─vdiffr:::print_plot(plot, title)
4. └─vdiffr:::print_plot.function(plot, title)
5. └─Ternary (local) p()
6. └─Ternary::Annotate(ptsList[1:2], side = 1, outset = 0.2) at test-Annotate.R:12:5
7. └─TreeDist::LAPJV(euclid)
8. └─TreeDist:::lapjv(x, max(x))
[ FAIL 1 | WARN 1 | SKIP 10 | PASS 117 ]
Deleting unused snapshots: 'Annotate/annotate-auto-locate.svg' and
'Annotate/annotate-zoomed.svg'
Error:
! Test failures.
Execution halted
Flavor: r-release-macos-x86_64
Version: 2.3.6
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Holdridge.Rmd’ using rmarkdown
--- finished re-building ‘Holdridge.Rmd’
--- re-building ‘Ternary.Rmd’ using rmarkdown
--- finished re-building ‘Ternary.Rmd’
--- re-building ‘annotation.Rmd’ using rmarkdown
Quitting from annotation.Rmd:36-48 [auto-annotate]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `lapjv()`:
! object '_TreeDist_lapjv' not found
---
Backtrace:
▆
1. └─Ternary::Annotate(points[, 1:3], col = points[, "col"])
2. └─TreeDist::LAPJV(euclid)
3. └─TreeDist:::lapjv(x, max(x))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'annotation.Rmd' failed with diagnostics:
object '_TreeDist_lapjv' not found
--- failed re-building ‘annotation.Rmd’
--- re-building ‘interpolation.Rmd’ using rmarkdown
--- finished re-building ‘interpolation.Rmd’
--- re-building ‘new-users.Rmd’ using rmarkdown
--- finished re-building ‘new-users.Rmd’
SUMMARY: processing the following file failed:
‘annotation.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64
Current CRAN status: NOTE: 2, OK: 11
Version: 2.0.1
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Martin R. Smith <martin.smith@durham.ac.uk>’
Package CITATION file contains call(s) to old-style personList() or
as.personList(). Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry(). Please
use bibentry() instead.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 1.7.0
Check: examples
Result: ERROR
Running examples in ‘TreeSearch-Ex.R’ failed
The error most likely occurred in:
> ### Name: SiteConcordance
> ### Title: Calculate site concordance factor
> ### Aliases: SiteConcordance QuartetConcordance ClusteringConcordance
> ### PhylogeneticConcordance MutualClusteringConcordance
> ### SharedPhylogeneticConcordance
>
> ### ** Examples
>
> data("congreveLamsdellMatrices", package = "TreeSearch")
> dataset <- congreveLamsdellMatrices[[1]][, 1:20]
> tree <- referenceTree
> qc <- QuartetConcordance(tree, dataset)
> cc <- ClusteringConcordance(tree, dataset)
> pc <- PhylogeneticConcordance(tree, dataset)
> spc <- SharedPhylogeneticConcordance(tree, dataset)
Error in PairScorer(splits1, splits2, nTip, ...) :
object '_TreeDist_cpp_shared_phylo' not found
Calls: SharedPhylogeneticConcordance ... vapply -> FUN -> Func -> GeneralizedRF -> PairScorer
Execution halted
Flavor: r-release-macos-x86_64
Version: 1.7.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [55s/83s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library("testthat")
> library("TreeSearch")
>
> test_check("TreeSearch")
Saving _problems/test-TaxonInfluence-9.R
Saving _problems/test-TaxonInfluence-35.R
1 + 0 != 10
[ FAIL 2 | WARN 0 | SKIP 5 | PASS 7340 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On CRAN (4): 'test-Jackknife.R:27:1', 'test-PlotCharacter.R:1:1',
'test-PlotCharacter.R:141:1', 'test-PlotCharacter.R:151:1'
• Sys.getenv("GITHUB_PAT") == "" is TRUE (1): 'test-MaximizeParsimony.R:71:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-TaxonInfluence.R:9:3'): TaxonInfluence() works ─────────────────
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_mutual_clustering' not found
Backtrace:
▆
1. └─TreeSearch::TaxonInfluence(...) at test-TaxonInfluence.R:9:3
2. ├─base::rowSums(as.matrix(Distance(tree)))
3. │ └─base::is.data.frame(x)
4. ├─base::as.matrix(Distance(tree))
5. └─TreeDist (local) Distance(tree)
6. └─TreeDist::MutualClusteringInfo(...)
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-TaxonInfluence.R:34:3'): TaxonInfluence() saves intermediate trees ──
Error in `PairScorer(splits1, splits2, nTip, ...)`: object '_TreeDist_cpp_mutual_clustering' not found
Backtrace:
▆
1. └─TreeSearch::TaxonInfluence(...) at test-TaxonInfluence.R:34:3
2. └─base::vapply(...)
3. └─TreeSearch (local) FUN(X[[i]], ...)
4. ├─base::matrix(Distance(tree, result), length(result))
5. └─TreeDist (local) Distance(tree, result)
6. └─TreeDist::MutualClusteringInfo(...)
7. └─TreeDist::CalculateTreeDistance(...)
8. └─TreeDist:::.SplitDistanceOneMany(...)
9. ├─stats::setNames(...)
10. ├─base::unlist(...)
11. └─base::.mapply(...)
12. └─TreeDist (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
13. └─TreeDist (local) Func(...)
14. └─TreeDist::GeneralizedRF(...)
15. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
[ FAIL 2 | WARN 0 | SKIP 5 | PASS 7340 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-macos-x86_64
Version: 1.7.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘custom.Rmd’ using rmarkdown
Quitting from custom.Rmd:84-105 [cid]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `PairScorer()`:
! object '_TreeDist_cpp_mutual_clustering' not found
---
Backtrace:
▆
1. └─TreeSearch::TreeSearch(...)
2. └─TreeSearch::EdgeListSearch(...)
3. └─global TreeScorer(edgeList[[1]], edgeList[[2]], dataset, ...)
4. └─TreeDist::ClusteringInfoDistance(startTree, tmpTree)
5. └─TreeDist::MutualClusteringInfo(...)
6. └─TreeDist::CalculateTreeDistance(...)
7. └─TreeDist:::.SplitDistanceOneOne(...)
8. └─TreeDist (local) Func(...)
9. └─TreeDist::GeneralizedRF(...)
10. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'custom.Rmd' failed with diagnostics:
object '_TreeDist_cpp_mutual_clustering' not found
--- failed re-building ‘custom.Rmd’
--- re-building ‘getting-started.Rmd’ using rmarkdown
--- finished re-building ‘getting-started.Rmd’
--- re-building ‘profile-scores.Rmd’ using rmarkdown
--- finished re-building ‘profile-scores.Rmd’
--- re-building ‘profile.Rmd’ using rmarkdown
--- finished re-building ‘profile.Rmd’
--- re-building ‘tree-search.Rmd’ using rmarkdown
Quitting from tree-search.Rmd:102-115 [map-search]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `PairScorer()`:
! object '_TreeDist_cpp_mutual_clustering' not found
---
Backtrace:
▆
1. └─TreeDist::ClusteringInfoDistance(bestTrees)
2. └─TreeDist::MutualClusteringInfo(...)
3. └─TreeDist::CalculateTreeDistance(...)
4. └─TreeDist:::.SplitDistanceAllPairs(...)
5. ├─base::structure(...)
6. └─base::apply(is, 2, .CliPairDist)
7. └─TreeDist (local) FUN(newX[, i], ...)
8. └─TreeDist (local) .PairDist(i)
9. └─TreeDist (local) Func(...)
10. └─TreeDist::GeneralizedRF(...)
11. └─TreeDist (local) PairScorer(splits1, splits2, nTip, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'tree-search.Rmd' failed with diagnostics:
object '_TreeDist_cpp_mutual_clustering' not found
--- failed re-building ‘tree-search.Rmd’
--- re-building ‘tree-space.Rmd’ using rmarkdown
Quitting from tree-space.Rmd:93-141 [exploring-consensus]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `consensus_info()`:
! object '_TreeDist_consensus_info' not found
---
Backtrace:
▆
1. └─Rogue::QuickRogue(trees, p = majority)
2. └─TreeDist::ConsensusInfo(trees, info = info, p = p, check.tips = FALSE)
3. └─TreeDist:::consensus_info(trees, mode == 1L, p = safeP)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'tree-space.Rmd' failed with diagnostics:
object '_TreeDist_consensus_info' not found
--- failed re-building ‘tree-space.Rmd’
SUMMARY: processing the following files failed:
‘custom.Rmd’ ‘tree-search.Rmd’ ‘tree-space.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64
Current CRAN status: WARN: 1, OK: 12
Version: 2.3.0
Check: Rd files
Result: WARN
2026-04-25 01:23:04.120 R[24344:184991] XType: Using static font registry.
Flavor: r-oldrel-macos-arm64