Last updated on 2026-08-03 03:51:07 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.7.0 | 29.04 | 272.42 | 301.46 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.7.0 | 23.46 | 187.02 | 210.48 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.7.0 | 45.00 | 437.32 | 482.32 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.7.0 | 28.00 | 196.20 | 224.20 | NOTE | |
| r-devel-windows-x86_64 | 1.7.0 | 46.00 | 283.00 | 329.00 | NOTE | |
| r-patched-linux-x86_64 | 1.7.0 | 34.29 | 260.74 | 295.03 | OK | |
| r-release-linux-x86_64 | 1.7.0 | 28.41 | 260.29 | 288.70 | OK | |
| r-release-macos-arm64 | 1.7.0 | 7.00 | 63.00 | 70.00 | OK | |
| r-release-macos-x86_64 | 1.7.0 | 60.00 | 758.00 | 818.00 | ERROR | |
| r-release-windows-x86_64 | 1.7.0 | 49.00 | 302.00 | 351.00 | OK | |
| r-oldrel-macos-arm64 | 1.7.0 | OK | ||||
| r-oldrel-macos-x86_64 | 1.7.0 | 21.00 | 265.00 | 286.00 | OK | |
| r-oldrel-windows-x86_64 | 1.7.0 | 60.00 | 394.00 | 454.00 | OK |
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: for new files in some other directories
Result: NOTE
Found the following files/directories:
‘~/tmp/scratch/Rtmp035JiU’ ‘~/tmp/scratch/Rtmp09WWoj’
‘~/tmp/scratch/Rtmp0oUTiw’ ‘~/tmp/scratch/Rtmp2ATdPT’
‘~/tmp/scratch/Rtmp2dRzqV’ ‘~/tmp/scratch/Rtmp2hF3N3’
‘~/tmp/scratch/Rtmp3A0zEm’ ‘~/tmp/scratch/Rtmp3RMxP0’
‘~/tmp/scratch/Rtmp3nXABN’ ‘~/tmp/scratch/Rtmp402Q0v’
‘~/tmp/scratch/Rtmp4pPbao’ ‘~/tmp/scratch/Rtmp5hrDBm’
‘~/tmp/scratch/Rtmp7WQPWr’ ‘~/tmp/scratch/Rtmp7kgpPZ’
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‘~/tmp/scratch/Rtmp8fA7Ul’ ‘~/tmp/scratch/Rtmp8n02AP’
‘~/tmp/scratch/Rtmp8pFJak’ ‘~/tmp/scratch/Rtmp8wK73f’
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‘~/tmp/scratch/Rtmpr9ZA6m’ ‘~/tmp/scratch/RtmprSNF7W’
‘~/tmp/scratch/RtmptVtHvL’ ‘~/tmp/scratch/RtmptydUo1’
‘~/tmp/scratch/Rtmpu1DvgO’ ‘~/tmp/scratch/RtmpuVeriN’
‘~/tmp/scratch/Rtmpuc2cUZ’ ‘~/tmp/scratch/RtmpuvMRMf’
‘~/tmp/scratch/Rtmpvsen14’ ‘~/tmp/scratch/RtmpwKxwNh’
‘~/tmp/scratch/RtmpwT7RPC’ ‘~/tmp/scratch/RtmpwmvwMP’
‘~/tmp/scratch/Rtmpx4Z7rb’ ‘~/tmp/scratch/Rtmpx9MIfN’
‘~/tmp/scratch/RtmpxgePkb’ ‘~/tmp/scratch/Rtmpxhogad’
‘~/tmp/scratch/RtmpxuXNlM’ ‘~/tmp/scratch/RtmpyWjtRm’
‘~/tmp/scratch/RtmpypRmiN’ ‘~/tmp/scratch/RtmpzGouVP’
‘~/tmp/scratch/RtmpzgTG6n’ ‘~/tmp/scratch/xvfb-run.06Lnwd’
‘~/tmp/scratch/xvfb-run.0neYcs’ ‘~/tmp/scratch/xvfb-run.2SQ6hj’
‘~/tmp/scratch/xvfb-run.3OlIjk’ ‘~/tmp/scratch/xvfb-run.4O7pnt’
‘~/tmp/scratch/xvfb-run.58iBrt’ ‘~/tmp/scratch/xvfb-run.5WKtN0’
‘~/tmp/scratch/xvfb-run.6Gx8PO’ ‘~/tmp/scratch/xvfb-run.6QSIrh’
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‘~/tmp/scratch/xvfb-run.cGfX5V’ ‘~/tmp/scratch/xvfb-run.cUfKaS’
‘~/tmp/scratch/xvfb-run.dAhk62’ ‘~/tmp/scratch/xvfb-run.eQB9zw’
‘~/tmp/scratch/xvfb-run.f76d0q’ ‘~/tmp/scratch/xvfb-run.g0Oxb6’
‘~/tmp/scratch/xvfb-run.jFsoXP’ ‘~/tmp/scratch/xvfb-run.jph4w0’
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Flavor: r-devel-linux-x86_64-debian-gcc
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