Last updated on 2026-08-04 14:52:37 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.7.0 | 29.84 | 272.71 | 302.55 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.7.0 | 25.00 | 183.24 | 208.24 | 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 | 46.00 | 293.00 | 339.00 | 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 | 500.00 | 560.00 | 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/Rtmp0k6pji’ ‘~/tmp/scratch/Rtmp0o4Hj1’
‘~/tmp/scratch/Rtmp1Ub1aa’ ‘~/tmp/scratch/Rtmp1lEeWb’
‘~/tmp/scratch/Rtmp3OIAf8’ ‘~/tmp/scratch/Rtmp3VbgLe’
‘~/tmp/scratch/Rtmp41kGHn’ ‘~/tmp/scratch/Rtmp44Eftz’
‘~/tmp/scratch/Rtmp4DhfTd’ ‘~/tmp/scratch/Rtmp5Ouqls’
‘~/tmp/scratch/Rtmp5ahqNx’ ‘~/tmp/scratch/Rtmp6dD0jG’
‘~/tmp/scratch/Rtmp6k8tcN’ ‘~/tmp/scratch/Rtmp7JTTBw’
‘~/tmp/scratch/Rtmp7biC7U’ ‘~/tmp/scratch/Rtmp8Rr4iN’
‘~/tmp/scratch/Rtmp9BZwZF’ ‘~/tmp/scratch/Rtmp9Kkp0h’
‘~/tmp/scratch/Rtmp9XdXq6’ ‘~/tmp/scratch/RtmpA417Wl’
‘~/tmp/scratch/RtmpB1ZGOK’ ‘~/tmp/scratch/RtmpBFdjxT’
‘~/tmp/scratch/RtmpBI6FCz’ ‘~/tmp/scratch/RtmpBhnjxs’
‘~/tmp/scratch/RtmpCD9Zqg’ ‘~/tmp/scratch/RtmpCbDjGW’
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‘~/tmp/scratch/RtmpDSiaIR’ ‘~/tmp/scratch/RtmpDjpUah’
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‘~/tmp/scratch/RtmpE81wpQ’ ‘~/tmp/scratch/RtmpEGblkn’
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‘~/tmp/scratch/RtmpFI2itO’ ‘~/tmp/scratch/RtmpFQ85lI’
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‘~/tmp/scratch/RtmpGQHX7n’ ‘~/tmp/scratch/RtmpGRvyMe’
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‘~/tmp/scratch/xvfb-run.u5zxYc’ ‘~/tmp/scratch/xvfb-run.uwix53’
‘~/tmp/scratch/xvfb-run.vY6PGP’ ‘~/tmp/scratch/xvfb-run.vt4YKH’
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‘~/tmp/scratch/xvfb-run.zHy1Mg’ ‘~/tmp/scratch/xvfb-run.zP58Dx’
‘~/tmp/scratch/xvfb-run.zxXiIm’
‘/dev/shm/0d10ac10-0fcf-4671-bd2e-374051628659’
‘/dev/shm/0d10ac10-0fcf-4671-bd2e-374051628659_counter’
‘/dev/shm/1b17a7cb-54b7-4dd4-b131-ef81121ce06e’
‘/dev/shm/1b17a7cb-54b7-4dd4-b131-ef81121ce06e_counter’
‘/dev/shm/1f11db57-d5a9-495a-9986-9d4166b0f033’
‘/dev/shm/1f11db57-d5a9-495a-9986-9d4166b0f033_counter’
‘/dev/shm/281e2bb4-3a43-4d5f-ac71-2e4c2e1bbc0b’
‘/dev/shm/281e2bb4-3a43-4d5f-ac71-2e4c2e1bbc0b_counter’
‘/dev/shm/2a58f230-a656-45bb-9964-3dd672cfbf0b’
‘/dev/shm/2a58f230-a656-45bb-9964-3dd672cfbf0b_counter’
‘/dev/shm/3f8b85cb-21f0-430e-a63d-a40b067bd7f5’
‘/dev/shm/3f8b85cb-21f0-430e-a63d-a40b067bd7f5_counter’
‘/dev/shm/403c32f9-43d6-4685-831a-31a487fdb06d’
‘/dev/shm/403c32f9-43d6-4685-831a-31a487fdb06d_counter’
‘/dev/shm/42142167-f053-4fab-afaf-23859916f8fb’
‘/dev/shm/42142167-f053-4fab-afaf-23859916f8fb_counter’
‘/dev/shm/5f16aabe-61a9-4fa4-92f8-be0e423c5876’
‘/dev/shm/5f16aabe-61a9-4fa4-92f8-be0e423c5876_counter’
‘/dev/shm/8e320a81-7a76-4e43-ad61-41d9bc209fd1’
‘/dev/shm/8e320a81-7a76-4e43-ad61-41d9bc209fd1_counter’
‘/dev/shm/ac7fe6f2-992f-4568-bd1f-7cf2cff58dcd’
‘/dev/shm/ac7fe6f2-992f-4568-bd1f-7cf2cff58dcd_counter’
‘/dev/shm/add50864-c7df-4a81-b05b-9cfd9bf4a84e’
‘/dev/shm/add50864-c7df-4a81-b05b-9cfd9bf4a84e_counter’
‘/dev/shm/ae324dd6-d049-4afb-9a00-fe4d9ebeda1d’
‘/dev/shm/ae324dd6-d049-4afb-9a00-fe4d9ebeda1d_counter’
‘/dev/shm/d26d3e27-15ac-4182-a60a-24a25aa6dd34’
‘/dev/shm/d26d3e27-15ac-4182-a60a-24a25aa6dd34_counter’
‘/dev/shm/d68dafe6-2db0-4098-b4de-21dc94459762’
‘/dev/shm/d68dafe6-2db0-4098-b4de-21dc94459762_counter’
‘/dev/shm/sem.0d10ac10-0fcf-4671-bd2e-374051628659_bigmemory_counter_mutex’
‘/dev/shm/sem.1b17a7cb-54b7-4dd4-b131-ef81121ce06e_bigmemory_counter_mutex’
‘/dev/shm/sem.1f11db57-d5a9-495a-9986-9d4166b0f033_bigmemory_counter_mutex’
‘/dev/shm/sem.281e2bb4-3a43-4d5f-ac71-2e4c2e1bbc0b_bigmemory_counter_mutex’
‘/dev/shm/sem.2a58f230-a656-45bb-9964-3dd672cfbf0b_bigmemory_counter_mutex’
‘/dev/shm/sem.3f8b85cb-21f0-430e-a63d-a40b067bd7f5_bigmemory_counter_mutex’
‘/dev/shm/sem.403c32f9-43d6-4685-831a-31a487fdb06d_bigmemory_counter_mutex’
‘/dev/shm/sem.42142167-f053-4fab-afaf-23859916f8fb_bigmemory_counter_mutex’
‘/dev/shm/sem.4e149c04-9902-4ac2-81a1-2cd98e77dbef_bigmemory_counter_mutex’
‘/dev/shm/sem.5f16aabe-61a9-4fa4-92f8-be0e423c5876_bigmemory_counter_mutex’
‘/dev/shm/sem.8e320a81-7a76-4e43-ad61-41d9bc209fd1_bigmemory_counter_mutex’
‘/dev/shm/sem.91156269-33a1-4367-8a67-f2cf1cb5abf6_bigmemory_counter_mutex’
‘/dev/shm/sem.ac7fe6f2-992f-4568-bd1f-7cf2cff58dcd_bigmemory_counter_mutex’
‘/dev/shm/sem.add50864-c7df-4a81-b05b-9cfd9bf4a84e_bigmemory_counter_mutex’
‘/dev/shm/sem.ae324dd6-d049-4afb-9a00-fe4d9ebeda1d_bigmemory_counter_mutex’
‘/dev/shm/sem.b6c187f4-6e50-40fc-ad43-9b6783d5fe00_bigmemory_counter_mutex’
‘/dev/shm/sem.bd13d726-f7c1-424a-bc37-65c03974f9a4_bigmemory_counter_mutex’
‘/dev/shm/sem.d26d3e27-15ac-4182-a60a-24a25aa6dd34_bigmemory_counter_mutex’
‘/dev/shm/sem.d68dafe6-2db0-4098-b4de-21dc94459762_bigmemory_counter_mutex’
‘/dev/shm/sem.f48cea97-192b-41a2-a5fb-d48dca4e7b69_bigmemory_counter_mutex’
‘/dev/shm/sem.fe06888a-bc80-4aef-89e3-c98c20565edb_bigmemory_counter_mutex’
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