Check results for 'Rogue'

using R version 4.6.0 (2026-04-24)
using platform: x86_64-apple-darwin20
R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0
running under: macOS Ventura 13.3.1
using session charset: UTF-8 * current time: 2026-04-28 20:51:50 UTC
checking for file ‘Rogue/DESCRIPTION’ ... OK
this is package ‘Rogue’ version ‘2.2.0’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
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checking whether package ‘Rogue’ can be installed ... [47s/92s] OK See the install log for details.
used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
used SDK: ‘MacOSX11.3.1.sdk’
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checking examples ... [13s/28s] 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
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [20s/34s] 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
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [29s/52s] 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
checking PDF version of manual ... [6s/9s] OK
DONE Status: 3 ERRORs
using check arguments '--no-clean-on-error '