• using R version 4.6.2 (2026-10-29)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.2.0-3) 16.2.0     GNU Fortran (Debian 16.2.0-3) 16.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-11-07 20:47:47 UTC
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• this is package ‘pre’ version ‘1.1.1’
• package encoding: UTF-8
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• checking whether package ‘pre’ can be installed ... OK See the install log for details.
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• checking tests ... [37s/72s] ERROR   Running ‘testthat.R’ [37s/71s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(pre)   >   > #####   > # partykit and earth is loaded as failures of tests may be caused by the version   > # of either package. Thus, we print the sessionInfo   >   > library(earth)   Loading required package: Formula   Loading required package: plotmo   Loading required package: plotrix   > library(partykit)   Loading required package: grid   Loading required package: libcoin   Loading required package: mvtnorm   > library(mlbench)   > library(glmnet)   Loading required package: Matrix   Loaded glmnet 5.2   > print(sessionInfo())   R version 4.6.2 (2026-10-29)   Platform: x86_64-pc-linux-gnu   Running under: Debian GNU/Linux forky/sid      Matrix products: default   BLAS: /home/hornik/tmp/R.check/r-release-gcc/Work/build/lib/libRblas.so   LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.1; LAPACK version 3.12.0      locale:    [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8    [4] LC_COLLATE=C LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8    [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C   [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C      time zone: Europe/Vienna   tzcode source: system (glibc)      attached base packages:   [1] grid stats graphics grDevices utils datasets methods   [8] base      other attached packages:    [1] glmnet_5.2 Matrix_1.7-6 mlbench_2.1-11 partykit_1.3-1 mvtnorm_1.4-2    [6] libcoin_1.0-13 earth_5.3.6 plotmo_3.7.1 plotrix_3.8-14 Formula_1.2-6   [11] pre_1.1.1 testthat_3.3.2      loaded via a namespace (and not attached):    [1] cli_3.6.6 rlang_1.3.0 stringi_1.8.9 otel_0.2.0    [5] MatrixModels_0.5-4 glue_1.8.1 zoo_1.9-1 brio_1.1.5    [9] foreach_1.5.2 lifecycle_1.0.5 stringr_1.6.0 compiler_4.6.2   [13] strucchange_1.6-0 codetools_0.2-20 sandwich_3.1-3 Rcpp_1.1.2   [17] lattice_0.23-1 R6_2.6.1 splines_4.6.2 inum_1.0-5   [21] shape_1.4.6.1 magrittr_2.0.5 rpart_4.1.27 tools_4.6.2   [25] iterators_1.0.14 survival_3.8-12   >   > test_check("pre")   Saving _problems/test_gpe-11.R   Saving _problems/test_gpe-455.R   Saving _problems/test_gpe_misc-14.R   Saving _problems/test_gpe_misc-48.R   Saving _problems/test_gpe_misc-63.R   Saving _problems/test_pre_misc-37.R   Saving _problems/tests_pre-60.R   Saving _problems/tests_pre-72.R   Saving _problems/tests_pre-80.R   Saving _problems/tests_pre-89.R   [ FAIL 12 | WARN 0 | SKIP 0 | PASS 112 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test_gpe.R:7:3'): gpe works with default settings and gives previous results ──   Error: Unknown control parameter(s) in cv.glmnet(): thres     Valid keys: thresh, maxit, dfmax, pmax, trace.it, fdev, devmax, eps, big, mnlam, pmin, exmx, prec, mxit, itrace, epsnr, mxitnr   Backtrace:       ▆    1. └─pre::gpe(Ozone ~ ., data = airquality, base_learners = list(gpe_trees(ntrees = 10))) at test_gpe.R:7:3    2. └─pre (local) penalized_trainer(x = x, y = y, family = family, weights = weights)    3. ├─base::do.call(cv.glmnet, call_args)    4. └─glmnet (local) `<fn>`(...)    5. └─glmnet:::.validate_control_keys(control, where = "cv.glmnet()")   ── Error ('test_gpe.R:39:3'): gpe works with factor predictor and gpe_linear ───   Error: Unknown control parameter(s) in cv.glmnet(): thres     Valid keys: thresh, maxit, dfmax, pmax, trace.it, fdev, devmax, eps, big, mnlam, pmin, exmx, prec, mxit, itrace, epsnr, mxitnr   Backtrace:        ▆     1. ├─testthat::expect_silent(fit <- gpe(y ~ ., dat, base_learners = list(gpe_linear()))) at test_gpe.R:39:3     2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)     3. │ ├─testthat (local) .capture(...)     4. │ │ ├─withr::with_output_sink(...)     5. │ │ │ └─base::force(code)     6. │ │ ├─base::withCallingHandlers(...)     7. │ │ └─base::withVisible(code)     8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     9. └─pre::gpe(y ~ ., dat, base_learners = list(gpe_linear()))    10. └─pre (local) penalized_trainer(x = x, y = y, family = family, weights = weights)    11. ├─base::do.call(cv.glmnet, call_args)    12. └─glmnet (local) `<fn>`(...)    13. └─glmnet:::.validate_control_keys(control, where = "cv.glmnet()")   ── Error ('test_gpe.R:455:3'): gpe_cv.glmnet gives same results as cv.glmnet ───   Error: Unknown control parameter(s) in cv.glmnet(): thres     Valid keys: thresh, maxit, dfmax, pmax, trace.it, fdev, devmax, eps, big, mnlam, pmin, exmx, prec, mxit, itrace, epsnr, mxitnr   Backtrace:       ▆    1. ├─base::do.call(glmnet::cv.glmnet, def) at test_gpe.R:455:3    2. └─glmnet (local) `<fn>`(...)    3. └─glmnet:::.validate_control_keys(control, where = "cv.glmnet()")   ── Error ('test_gpe_misc.R:11:3'): Print works for gpe ─────────────────────────   Error: Unknown control parameter(s) in cv.glmnet(): thres     Valid keys: thresh, maxit, dfmax, pmax, trace.it, fdev, devmax, eps, big, mnlam, pmin, exmx, prec, mxit, itrace, epsnr, mxitnr   Backtrace:       ▆    1. └─pre::gpe(Ozone ~ ., data = airquality, base_learners = list(gpe_linear())) at test_gpe_misc.R:11:3    2. └─pre (local) penalized_trainer(x = x, y = y, family = family, weights = weights)    3. ├─base::do.call(cv.glmnet, call_args)    4. └─glmnet (local) `<fn>`(...)    5. └─glmnet:::.validate_control_keys(control, where = "cv.glmnet()")   ── Error ('test_gpe_misc.R:45:3'): Coef works for gpe ──────────────────────────   Error: Unknown control parameter(s) in cv.glmnet(): thres     Valid keys: thresh, maxit, dfmax, pmax, trace.it, fdev, devmax, eps, big, mnlam, pmin, exmx, prec, mxit, itrace, epsnr, mxitnr   Backtrace:       ▆    1. └─pre::gpe(Ozone ~ ., data = airquality, base_learners = list(gpe_trees(ntrees = 10))) at test_gpe_misc.R:45:3    2. └─pre (local) penalized_trainer(x = x, y = y, family = family, weights = weights)    3. ├─base::do.call(cv.glmnet, call_args)    4. └─glmnet (local) `<fn>`(...)    5. └─glmnet:::.validate_control_keys(control, where = "cv.glmnet()")   ── Error ('test_gpe_misc.R:60:3'): Predict works for gpe and gives previous results ──   Error: Unknown control parameter(s) in cv.glmnet(): thres     Valid keys: thresh, maxit, dfmax, pmax, trace.it, fdev, devmax, eps, big, mnlam, pmin, exmx, prec, mxit, itrace, epsnr, mxitnr   Backtrace:       ▆    1. └─pre::gpe(Ozone ~ ., data = airquality, base_learners = list(gpe_trees(ntrees = 10))) at test_gpe_misc.R:60:3    2. └─pre (local) penalized_trainer(x = x, y = y, family = family, weights = weights)    3. ├─base::do.call(cv.glmnet, call_args)    4. └─glmnet (local) `<fn>`(...)    5. └─glmnet:::.validate_control_keys(control, where = "cv.glmnet()")   ── Error ('test_pre_misc.R:36:3'): gpe_rules_pre gives same results as pre with airquality data ──   Error: Unknown control parameter(s) in cv.glmnet(): thres     Valid keys: thresh, maxit, dfmax, pmax, trace.it, fdev, devmax, eps, big, mnlam, pmin, exmx, prec, mxit, itrace, epsnr, mxitnr   Backtrace:       ▆    1. └─pre::gpe(...) at test_pre_misc.R:36:3    2. └─pre (local) penalized_trainer(x = x, y = y, family = family, weights = weights)    3. ├─base::do.call(cv.glmnet, call_args)    4. └─glmnet (local) `<fn>`(...)    5. └─glmnet:::.validate_control_keys(control, where = "cv.glmnet()")   ── Failure ('tests_pre.R:60:3'): Get previous results with airquality and pre function ──   Expected `airq.ens` to equal `read_to_test("airquality_w_pre_with_glmtree")`.   Differences:   Component "glmnet.fit": Component "nzero": names for current but not for target   ── Failure ('tests_pre.R:72:3'): Get previous results with airquality and pre function ──   Expected `airq.ens.offs` to equal `read_to_test("airquality_w_pre_with_glmtree_w_offset")`.   Differences:   Component "glmnet.fit": Component "nzero": names for current but not for target   ── Failure ('tests_pre.R:80:3'): Get previous results with airquality and pre function ──   Expected `airq.ens` to equal `read_to_test("airquality_w_pre_with_adaptive_lasso")`.   Differences:   Component "glmnet.fit": Component "nzero": names for current but not for target   ── Failure ('tests_pre.R:89:3'): Get previous results with airquality and pre function ──   Expected `airq.ens` to equal `read_to_test("airquality_w_pre_with_relaxed_adaptive_lasso")`.   Differences:   Component "glmnet.fit": Component "nzero": names for current but not for target   Component "glmnet.fit": Component "relaxed": Component "statlist": Component "g:0": Component "nzero": names for current but not for target   Component "glmnet.fit": Component "relaxed": Component "statlist": Component "g:0.25": Component "nzero": names for current but not for target   Component "glmnet.fit": Component "relaxed": Component "statlist": Component "g:0.5": Component "nzero": names for current but not for target   Component "glmnet.fit": Component "relaxed": Component "statlist": Component "g:0.75": Component "nzero": names for current but not for target   Component "glmnet.fit": Component "relaxed": Component "statlist": Component "g:1": Component "nzero": names for current but not for target   Component "glmnet.fit": Component "relaxed": Component "nzero.min": names for current but not for target   Component "glmnet.fit": Component "relaxed": Component "nzero.1se": names for current but not for target   ── Error ('tests_pre.R:93:3'): Get previous results with airquality and pre function ──   Error in `x[[jj]][iseq] <- vjj`: replacement has length zero   Backtrace:       ▆    1. ├─utils::capture.output(prune_pre(airq.ens, nonzero = 2)) at tests_pre.R:93:3    2. │ └─base::withVisible(...elt(i))    3. └─pre::prune_pre(airq.ens, nonzero = 2)    4. ├─base::`[<-`(`*tmp*`, i, "mean_cv_error", value = `<NULL>`)    5. └─base::`[<-.data.frame`(`*tmp*`, i, "mean_cv_error", value = `<NULL>`)      [ FAIL 12 | WARN 0 | SKIP 0 | PASS 112 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [195s/269s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘Missingness.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘Missingness.Rmd’ --- re-building ‘Tuning.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘Tuning.Rmd’ --- re-building ‘relaxed.Rmd’ using rmarkdown Quitting from relaxed.Rmd:164-166 [unnamed-chunk-8] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `x[[jj]][iseq] <- vjj`: ! replacement has length zero --- Backtrace:     ▆  1. └─pre::prune_pre(airq.ens.rel, nonzero = 5)  2. ├─base::`[<-`(`*tmp*`, i, "mean_cv_error", value = `<NULL>`)  3. └─base::`[<-.data.frame`(`*tmp*`, i, "mean_cv_error", value = `<NULL>`) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'relaxed.Rmd' failed with diagnostics: replacement has length zero --- failed re-building ‘relaxed.Rmd’ --- re-building ‘shap.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘shap.Rmd’ --- re-building ‘speed.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘speed.Rmd’ SUMMARY: processing the following file failed:   ‘relaxed.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [7s/9s] OK
• checking HTML version of manual ... [6s/9s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs