* using log directory ‘/Users/ripley/R/packages/tests-devel/fuseMLR.Rcheck’ * using R Under development (unstable) (2026-05-15 r90061) * using platform: aarch64-apple-darwin25.5.0 * R was compiled by Apple clang version 21.0.0 (clang-2100.1.1.101) GNU Fortran (GCC) 14.2.0 * running under: macOS Tahoe 26.5 * using session charset: UTF-8 * current time: 2026-05-16 10:11:10 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘fuseMLR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘fuseMLR’ version ‘0.0.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘fuseMLR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(fuseMLR) > > test_check("fuseMLR") Class : Data name : geneexpr ind. id. : IDS n : 49 p : 132 Class: HashTable id: test ----------------- [1] key class <0 rows> (or 0-length row.names) Learner : ranger TrainLayer : geneexpr Package : ranger Learn function : ranger Training of base model on layer geneexpr started. Training of base model on layer geneexpr done. Class : Model Learner info. ----------------------- Learner : ranger TrainLayer : geneexpr Package : ranger Learn function : ranger Train data info. ----------------------- TrainData : geneexpr Layer : geneexpr ind. id. : IDS target : disease n : 50 Missing : 0 p : 131 TrainLayer : geneexpr Status : Not trained Empty layer. TrainData : methylation Layer : methylation ind. id. : IDS target : disease n : 50 Missing : 0 p : 367 Layer geneexpr ---------------- TrainLayer : geneexpr Status : Not trained Empty layer. ---------------- Object(s) on layer geneexpr Empty layer Layer geneexpr ---------------- TrainLayer : geneexpr Status : Not trained Nb. of objects stored : 3 ---------------- Object(s) on layer geneexpr ---------------- Learner : ranger TrainLayer : geneexpr Package : ranger Learn function : ranger ---------------- ---------------- VarSel : varsel_geneexpr TrainLayer : geneexpr Package : Boruta Function : Boruta ---------------- ---------------- TrainData : geneexpr Layer : geneexpr Ind. id. : IDS Target : disease n : 50 Missing : 0 p : 131 ---------------- Training of base model on layer geneexpr started. Training of base model on layer geneexpr done. Layer geneexpr ---------------- TrainLayer : geneexpr Status : Trained Nb. of objects stored : 4 ---------------- Object(s) on layer geneexpr ---------------- Learner : ranger TrainLayer : geneexpr Package : ranger Learn function : ranger ---------------- ---------------- VarSel : varsel_geneexpr TrainLayer : geneexpr Package : Boruta Function : Boruta ---------------- ---------------- TrainData : geneexpr Layer : geneexpr Ind. id. : IDS Target : disease n : 50 Missing : 0 p : 131 ---------------- TrainMetaLayer : meta Status : Not trained Empty layer. MetaLayer ---------------- TrainMetaLayer : meta Status : Not trained Empty layer. ---------------- Object(s) on MetaLayer Empty layer Training : training Problem type : classification Status : Not trained Number of layers: 0 Layers trained : 0 Variable selection on layer geneexpr started. Saving _problems/test-Training-148.R VarSel : varsel_geneexpr TrainLayer : geneexpr Package : Boruta Function : Boruta Tuning 'epsilon' via cross-validation with 5 folds. Optimal epsilon: 0.071. Tuning with 5 folds. Tuning 'alpha' and 'epsilon' via cross-validation with 5 folds. Optimal alpha: 1 (1 Learner(s)). Optimal epsilon: 0.313. Tuning with 5 folds. Using user-defined 'epsilon' = 0.1. Tuning 'epsilon' via cross-validation with 10 folds. Tuning 'epsilon' via cross-validation with 10 folds. Tuning 'epsilon' via cross-validation with 10 folds. Tuning 'epsilon' via cross-validation with 10 folds. Tuning 'epsilon' via cross-validation with 10 folds. Tuning 'epsilon' via cross-validation with 10 folds. Optimal epsilon: 0.669. Tuning with 10 folds. Tuning 'alpha' and 'epsilon' via cross-validation with 10 folds. Optimal alpha: 1 (1 Learner(s)). Optimal epsilon: 0.217. Tuning with 10 folds. [ FAIL 1 | WARN 3 | SKIP 2 | PASS 170 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test-TrainMetaLayer.R:60:5', 'test-VarSel.R:43:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-Training.R:148:5'): Training: all tests ──────────────────────── Error in `fru::fru(x, y, trees = trees, importance = TRUE, threads = threads, ...)`: unused arguments (num.trees = 50, mtry = 3) Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-Training.R:141:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─training$varSelection() at test-Training.R:148:5 8. └─layer$varSelection(ind_subset = ind_subset, verbose = self$getVerbose()) 9. └─varsel$varSelection(ind_subset = ind_subset) 10. ├─base::do.call(eval(parse(text = varsel)), varsel_param) 11. ├─Boruta (local) ``(num.trees = 50L, mtry = 3L, x = ``, y = ``) 12. └─Boruta:::Boruta.default(...) 13. └─Boruta (local) addShadowsAndGetImp(decReg, runs) 14. └─Boruta (local) getImp(cbind(x[, decReg != "Rejected"], xSha), y, ...) 15. └─fru::importance(...) [ FAIL 1 | WARN 3 | SKIP 2 | PASS 170 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘fuseMLR.Rmd’ using rmarkdown Quitting from fuseMLR.Rmd:162-167 [varsel] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `fru::fru()`: ! unused arguments (num.trees = 1000, mtry = 3, probability = TRUE) --- Backtrace: ▆ 1. └─fuseMLR::varSelection(training = training) 2. └─training$varSelection(ind_subset = ind_subset, verbose = training$getVerbose()) 3. └─layer$varSelection(ind_subset = ind_subset, verbose = self$getVerbose()) 4. └─varsel$varSelection(ind_subset = ind_subset) 5. ├─base::do.call(eval(parse(text = varsel)), varsel_param) 6. ├─Boruta (local) ``(...) 7. └─Boruta:::Boruta.default(...) 8. └─Boruta (local) addShadowsAndGetImp(decReg, runs) 9. └─Boruta (local) getImp(cbind(x[, decReg != "Rejected"], xSha), y, ...) 10. └─fru::importance(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'fuseMLR.Rmd' failed with diagnostics: unused arguments (num.trees = 1000, mtry = 3, probability = TRUE) --- failed re-building ‘fuseMLR.Rmd’ SUMMARY: processing the following file failed: ‘fuseMLR.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs See ‘/Users/ripley/R/packages/tests-devel/fuseMLR.Rcheck/00check.log’ for details. 34.28 real 26.70 user 6.59 sys