Last updated on 2026-10-29 23:00:11 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.1 | 16.02 | 364.79 | 380.81 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.1 | 9.31 | 226.47 | 235.78 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.1 | 10.00 | 224.24 | 234.24 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.1 | 10.00 | 225.16 | 235.16 | ERROR | |
| r-devel-windows-x86_64 | 1.1.1 | 16.00 | 341.00 | 357.00 | OK | |
| r-patched-linux-x86_64 | 1.1.1 | 17.11 | 350.47 | 367.58 | OK | |
| r-release-linux-x86_64 | 1.1.1 | 14.92 | 345.30 | 360.22 | OK | |
| r-release-macos-arm64 | 1.1.1 | 5.00 | 82.00 | 87.00 | OK | |
| r-release-macos-x86_64 | 1.1.1 | 10.00 | 359.00 | 369.00 | OK | |
| r-release-windows-x86_64 | 1.1.1 | 16.00 | 324.00 | 340.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.1 | 3.00 | 90.00 | 93.00 | OK | |
| r-oldrel-macos-x86_64 | 1.1.1 | 10.00 | 381.00 | 391.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.1 | 21.00 | 456.00 | 477.00 | OK |
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [25s/44s]
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 Under development (unstable) (2026-10-28 r90783)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux forky/sid
Matrix products: default
BLAS: /home/hornik/tmp/R.check/r-devel-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_4.7.0
[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_4.7.0 inum_1.0-5
[21] shape_1.4.6.1 magrittr_2.0.5 rpart_4.1.27 tools_4.7.0
[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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.1
Check: re-building of vignette outputs
Result: 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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [25s/32s]
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 Under development (unstable) (2026-10-26 r90766)
Platform: x86_64-pc-linux-gnu
Running under: Fedora Linux 44 (Server Edition)
Matrix products: default
BLAS: /data/localhost/ripley/R/R-clang/lib/libRblas.so
LAPACK: /data/localhost/ripley/R/R-clang/lib/libRlapack.so; LAPACK version 3.12.1
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/London
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_4.7.0
[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_4.7.0 inum_1.0-5
[21] shape_1.4.6.1 magrittr_2.0.5 rpart_4.1.27 tools_4.7.0
[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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.1
Check: re-building of vignette outputs
Result: 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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [24s/34s]
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 Under development (unstable) (2026-10-28 r90767)
Platform: x86_64-pc-linux-gnu
Running under: Fedora Linux 44 (Server Edition)
Matrix products: default
BLAS: /data/localhost/ripley/R/R-devel/lib/libRblas.so
LAPACK: /usr/lib64/liblapack.so.3.12.0 LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/London
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_4.7.0
[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_4.7.0 inum_1.0-5
[21] shape_1.4.6.1 magrittr_2.0.5 rpart_4.1.27 tools_4.7.0
[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
Flavor: r-devel-linux-x86_64-fedora-gcc