Last updated on 2026-07-26 12:50:51 CEST.
| Package | OK | NOTE | WARN | ERROR |
|---|---|---|---|---|
| CongreveLamsdell2016 | 13 | |||
| ips | 8 | 5 | ||
| motmot | 13 | |||
| PlotTools | 13 | |||
| Quartet | 9 | 4 | ||
| Rogue | 13 | |||
| TBRDist | 13 | |||
| Ternary | 13 | |||
| TotalCopheneticIndex | 11 | 2 | ||
| TreeDist | 8 | 5 | ||
| TreeSearch | 8 | 4 | 1 | |
| TreeTools | 8 | 4 | 1 |
Current CRAN status: OK: 13
Current CRAN status: OK: 8, NOTE: 5
Version: 0.1.1
Check: R code for possible problems
Result: NOTE
Found calls to structure() using deprecated special names:
ips/man/trimEnds.Rd (.Names: 1)
'.Names' should be changed to 'names'.
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-devel-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 9, NOTE: 4
Version: 1.3.0
Check: R code for possible problems
Result: NOTE
Found calls to structure() using deprecated special names:
Quartet/tests/testthat/test-1-tqdist.R (.Dim: 1, .Dimnames: 1)
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 11, NOTE: 2
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: 8, NOTE: 5
Version: 2.14.1
Check: R code for possible problems
Result: NOTE
Found calls to structure() using deprecated special names:
TreeDist/tests/testthat/test-lap.R (.Dim: 2, .Dimnames: 2)
TreeDist/tests/testthat/test-mast.R (.Dim: 2)
TreeDist/tests/testthat/test-tree_distance.R (.Dim: 4)
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.
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-devel-windows-x86_64
Current CRAN status: OK: 8, NOTE: 4, ERROR: 1
Version: 1.7.0
Check: R code for possible problems
Result: NOTE
Found calls to structure() using deprecated special names:
TreeSearch/tests/testthat/test-PlotCharacter.R (.Dim: 1, .Dimnames: 1)
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
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: OK: 8, NOTE: 4, WARN: 1
Version: 2.4.0
Check: R code for possible problems
Result: NOTE
Found calls to structure() using deprecated special names:
TreeTools/tests/testthat/test-AddTip.R (.Dim: 1)
TreeTools/tests/testthat/test-DropTip.R (.Dim: 3)
TreeTools/tests/testthat/test-ImposeConstraint.R (.Dim: 1, .Dimnames: 1)
TreeTools/tests/testthat/test-ReadTntTree.R (.Dim: 1, .Dimnames: 1)
TreeTools/tests/testthat/test-Splits.R (.Dim: 8)
TreeTools/tests/testthat/test-TotalCopheneticIndex.R (.Dim: 1)
TreeTools/tests/testthat/test-consensus.R (.Dim: 1)
TreeTools/tests/testthat/test-parsers.R (.Dim: 1, .Dimnames: 1, .Label: 1)
TreeTools/tests/testthat/test-phylo.R (.Dim: 1)
TreeTools/tests/testthat/test-tree_numbering.R (.Dim: 5)
TreeTools/tests/testthat/test-tree_properties.R (.Dim: 1)
TreeTools/tests/testthat/test-tree_rearrange.R (.Dim: 11)
TreeTools/tests/testthat/test-tree_shape.R (.Dim: 1)
TreeTools/tests/testthat/test-tree_write.R (.Dim: 1)
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.
'.Label' should be changed to 'levels'.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Version: 2.4.0
Check: Rd files
Result: WARN
2026-06-03 09:26:43.684 R[6872:153327] XType: Using static font registry.
Flavor: r-oldrel-macos-arm64