* using log directory ‘/srv/hornik/tmp/CRAN_pretest/bonsai.Rcheck’ * using R Under development (unstable) (2025-02-08 r87709) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.6 (1+b1) Debian flang-new version 19.1.6 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘bonsai/DESCRIPTION’ ... OK * this is package ‘bonsai’ version ‘0.3.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/8s] OK * 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 ‘bonsai’ can be installed ... [3s/3s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking whether startup messages can be suppressed ... [1s/1s] 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 ... [5s/5s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [155s/8s] ERROR Running ‘testthat.R’ [155s/8s] Running R code in ‘testthat.R’ had CPU time 18.6 times elapsed time Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(bonsai) Loading required package: parsnip > > test_check("bonsai") [ FAIL 1 | WARN 0 | SKIP 6 | PASS 79 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • On CRAN (6): 'test-lightgbm.R:14:3', 'test-lightgbm.R:412:3', 'test-lightgbm.R:500:3', 'test-lightgbm.R:517:3', 'test-partykit.R:7:3', 'test-partykit.R:92:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-lightgbm.R:857:3'): sparse data with lightgbm ──────────────── `sprs_prob` (`actual`) not equal to `dens_prob` (`expected`). actual vs expected .pred_none .pred_mild .pred_severe - actual[1, ] 0.0418905792 0.956656113 1.453308e-03 + expected[1, ] 0.0418049571 0.956481296 1.713747e-03 - actual[2, ] 0.9573619762 0.042170504 4.675201e-04 + expected[2, ] 0.9559577107 0.043803739 2.385499e-04 - actual[3, ] 0.9924705196 0.007360886 1.685941e-04 + expected[3, ] 0.9932045031 0.006525370 2.701270e-04 - actual[4, ] 0.0184232868 0.007695235 9.738815e-01 + expected[4, ] 0.0219824460 0.007180594 9.708370e-01 - actual[5, ] 0.0389756083 0.959819903 1.204489e-03 + expected[5, ] 0.0419570332 0.955703564 2.339403e-03 - actual[6, ] 0.0044793583 0.011925043 9.835956e-01 + expected[6, ] 0.0035857850 0.012983947 9.834303e-01 - actual[7, ] 0.9735876348 0.026128243 2.841221e-04 + expected[7, ] 0.9641041501 0.035560821 3.350290e-04 - actual[8, ] 0.9758128883 0.024045141 1.419706e-04 + expected[8, ] 0.9752879214 0.024556133 1.559454e-04 - actual[9, ] 0.9792143227 0.020014680 7.709974e-04 + expected[9, ] 0.9719134102 0.025562739 2.523851e-03 - actual[10, ] 0.9711328442 0.026509111 2.358045e-03 + expected[10, ] 0.9533855410 0.038464554 8.149906e-03 and 271 more ... actual$.pred_none | expected$.pred_none [1] 0.0418906 - 0.0418050 [1] [2] 0.9573620 - 0.9559577 [2] [3] 0.9924705 - 0.9932045 [3] [4] 0.0184233 - 0.0219824 [4] [5] 0.0389756 - 0.0419570 [5] [6] 0.0044794 - 0.0035858 [6] [7] 0.9735876 - 0.9641042 [7] [8] 0.9758129 - 0.9752879 [8] [9] 0.9792143 - 0.9719134 [9] [10] 0.9711328 - 0.9533855 [10] ... ... ... and 271 more ... actual$.pred_mild | expected$.pred_mild [1] 0.956656 - 0.956481 [1] [2] 0.042171 - 0.043804 [2] [3] 0.007361 - 0.006525 [3] [4] 0.007695 - 0.007181 [4] [5] 0.959820 - 0.955704 [5] [6] 0.011925 - 0.012984 [6] [7] 0.026128 - 0.035561 [7] [8] 0.024045 - 0.024556 [8] [9] 0.020015 - 0.025563 [9] [10] 0.026509 - 0.038465 [10] ... ... ... and 271 more ... actual$.pred_severe | expected$.pred_severe [1] 0.0014533 - 0.0017137 [1] [2] 0.0004675 - 0.0002385 [2] [3] 0.0001686 - 0.0002701 [3] [4] 0.9738815 - 0.9708370 [4] [5] 0.0012045 - 0.0023394 [5] [6] 0.9835956 - 0.9834303 [6] [7] 0.0002841 - 0.0003350 [7] [8] 0.0001420 - 0.0001559 [8] [9] 0.0007710 - 0.0025239 [9] [10] 0.0023580 - 0.0081499 [10] ... ... ... and 271 more ... [ FAIL 1 | WARN 0 | SKIP 6 | PASS 79 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [33s/8s] NOTE Re-building vignettes had CPU time 3.9 times elapsed time * checking PDF version of manual ... [2s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE