Last updated on 2025-12-22 11:50:35 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.4 | 29.02 | 183.39 | 212.41 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2.4 | 18.34 | 114.71 | 133.05 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.4 | 61.00 | 451.40 | 512.40 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.4 | 53.00 | 268.30 | 321.30 | ERROR | |
| r-devel-windows-x86_64 | 0.2.4 | 35.00 | 164.00 | 199.00 | ERROR | |
| r-patched-linux-x86_64 | 0.2.4 | 27.45 | 147.16 | 174.61 | ERROR | |
| r-release-linux-x86_64 | 0.2.4 | 25.96 | 146.59 | 172.55 | ERROR | |
| r-release-macos-arm64 | 0.2.4 | OK | ||||
| r-release-macos-x86_64 | 0.2.4 | 17.00 | 423.00 | 440.00 | OK | |
| r-release-windows-x86_64 | 0.2.4 | 36.00 | 473.00 | 509.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.4 | OK | ||||
| r-oldrel-macos-x86_64 | 0.2.4 | 20.00 | 377.00 | 397.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.4 | 42.00 | 216.00 | 258.00 | ERROR |
Version: 0.2.4
Check: DESCRIPTION meta-information
Result: NOTE
Author field differs from that derived from Authors@R
Author: ‘Naeem Khoshnevis [aut] (<https://orcid.org/0000-0003-4315-1426>, HUIT), Boyu Ren [aut, cre] (<https://orcid.org/0000-0002-5300-1184>, McLean Hospital), Tanujit Dey [ctb] (<https://orcid.org/0000-0001-5559-211X>, HMS), Danielle Braun [aut] (<https://orcid.org/0000-0002-5177-8598>, HSPH)’
Authors@R: ‘Naeem Khoshnevis [aut] (ORCID: <https://orcid.org/0000-0003-4315-1426>, AFFILIATION: HUIT), Boyu Ren [aut, cre] (ORCID: <https://orcid.org/0000-0002-5300-1184>, AFFILIATION: McLean Hospital), Tanujit Dey [ctb] (ORCID: <https://orcid.org/0000-0001-5559-211X>, AFFILIATION: HMS), Danielle Braun [aut] (ORCID: <https://orcid.org/0000-0002-5177-8598>, AFFILIATION: HSPH)’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [50s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-19 17:36:41.893976 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_nn-8.R
2025-12-19 17:36:44.20513 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_weights_gp-8.R
2025-12-19 17:36:45.503346 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_m_sigma-12.R
2025-12-19 17:36:46.542619 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_m_nn-10.R
2025-12-19 17:36:47.557621 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_sd_nn-10.R
2025-12-19 17:36:48.605035 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_gp-8.R
2025-12-19 17:36:49.767825 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_nn-8.R
2025-12-19 17:36:50.89579 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_sd_gp-17.R
Saving _problems/test-compute_weight_gp-49.R
2025-12-19 17:36:52.563537 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_gp-10.R
2025-12-19 17:36:53.611697 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_nngp-10.R
2025-12-19 17:36:54.604827 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_gps-10.R
2025-12-19 17:36:55.746837 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_mean_sd_nn-10.R
2025-12-19 17:36:56.78894 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_gp-11.R
2025-12-19 17:36:58.104989 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_nn-10.R
2025-12-19 17:36:59.239186 gimli2 4144769 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-find_optimal_nn-9.R
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compute_deriv_nn.R:5:3'): compute_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_deriv_weights_gp.R:5:3'): compute_deriv_weights_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_weights_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_m_sigma.R:9:4'): compute_m_sigma works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_m_sigma.R:9:4
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_m_nn.R:7:3'): compute_posterior_m_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_m_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_sd_nn.R:7:3'): compute_posterior_sd_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_gp.R:5:3'): compute_rl_deriv_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_nn.R:5:3'): compute_rl_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_sd_gp.R:14:4'): compute_sd_gp works as expected. ───────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_sd_gp.R:14:4
2. └─SuperLearner::SuperLearner(...)
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Error ('test-estimate_cerf_gp.R:7:3'): estimate_cerf_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_gp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_cerf_nngp.R:7:3'): estimate_cerf_nngp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_nngp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_gps.R:7:3'): estimate_gps works as expected. ──────────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_gps.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_mean_sd_nn.R:7:3'): estimate_mean_sd_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_mean_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_gp.R:8:3'): estimate_noise_gp works as expected ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_gp.R:8:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_nn.R:7:3'): estimate_noise_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-find_optimal_nn.R:6:3'): find_optimal_nn works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-find_optimal_nn.R:6:3
2. └─SuperLearner::SuperLearner(...)
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘A-Note-on-Choosing-Hyperparameters.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘A-Note-on-Choosing-Hyperparameters.Rmd’
--- re-building ‘Developers-Guide.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Developers-Guide.Rmd’
--- re-building ‘GPCERF.Rmd’ using rmarkdown
2025-12-19 17:37:14.130352 gimli2 4154369 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from GPCERF.Rmd:38-45 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GPCERF.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘GPCERF.Rmd’
--- re-building ‘Nearest-neighbor-Gaussian-Processes.Rmd’ using rmarkdown
2025-12-19 17:37:25.447775 gimli2 4156280 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Nearest-neighbor-Gaussian-Processes.Rmd:83-92 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Nearest-neighbor-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘Nearest-neighbor-Gaussian-Processes.Rmd’
--- re-building ‘Standard-Gaussian-Processes.Rmd’ using rmarkdown
2025-12-19 17:37:37.189627 gimli2 4158657 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Standard-Gaussian-Processes.Rmd:83-93 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Standard-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘Standard-Gaussian-Processes.Rmd’
SUMMARY: processing the following files failed:
‘GPCERF.Rmd’ ‘Nearest-neighbor-Gaussian-Processes.Rmd’
‘Standard-Gaussian-Processes.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [23s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-21 13:25:00.235036 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_nn-8.R
2025-12-21 13:25:01.621574 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_weights_gp-8.R
2025-12-21 13:25:02.679117 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_m_sigma-12.R
2025-12-21 13:25:03.911578 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_m_nn-10.R
2025-12-21 13:25:04.746841 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_sd_nn-10.R
2025-12-21 13:25:05.620716 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_gp-8.R
2025-12-21 13:25:06.631357 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_nn-8.R
2025-12-21 13:25:07.469513 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_sd_gp-17.R
Saving _problems/test-compute_weight_gp-49.R
2025-12-21 13:25:09.619357 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_gp-10.R
2025-12-21 13:25:10.761354 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_nngp-10.R
2025-12-21 13:25:11.754282 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_gps-10.R
2025-12-21 13:25:12.721872 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_mean_sd_nn-10.R
2025-12-21 13:25:13.718323 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_gp-11.R
2025-12-21 13:25:14.818436 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_nn-10.R
2025-12-21 13:25:15.813971 gimli1 1252183 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-find_optimal_nn-9.R
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compute_deriv_nn.R:5:3'): compute_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_deriv_weights_gp.R:5:3'): compute_deriv_weights_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_weights_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_m_sigma.R:9:4'): compute_m_sigma works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_m_sigma.R:9:4
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_m_nn.R:7:3'): compute_posterior_m_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_m_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_sd_nn.R:7:3'): compute_posterior_sd_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_gp.R:5:3'): compute_rl_deriv_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_nn.R:5:3'): compute_rl_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_sd_gp.R:14:4'): compute_sd_gp works as expected. ───────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_sd_gp.R:14:4
2. └─SuperLearner::SuperLearner(...)
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Error ('test-estimate_cerf_gp.R:7:3'): estimate_cerf_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_gp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_cerf_nngp.R:7:3'): estimate_cerf_nngp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_nngp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_gps.R:7:3'): estimate_gps works as expected. ──────────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_gps.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_mean_sd_nn.R:7:3'): estimate_mean_sd_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_mean_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_gp.R:8:3'): estimate_noise_gp works as expected ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_gp.R:8:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_nn.R:7:3'): estimate_noise_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-find_optimal_nn.R:6:3'): find_optimal_nn works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-find_optimal_nn.R:6:3
2. └─SuperLearner::SuperLearner(...)
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘A-Note-on-Choosing-Hyperparameters.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘A-Note-on-Choosing-Hyperparameters.Rmd’
--- re-building ‘Developers-Guide.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Developers-Guide.Rmd’
--- re-building ‘GPCERF.Rmd’ using rmarkdown
2025-12-21 13:25:25.408788 gimli1 1267341 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from GPCERF.Rmd:38-45 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GPCERF.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘GPCERF.Rmd’
--- re-building ‘Nearest-neighbor-Gaussian-Processes.Rmd’ using rmarkdown
2025-12-21 13:25:32.21306 gimli1 1269190 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Nearest-neighbor-Gaussian-Processes.Rmd:83-92 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Nearest-neighbor-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘Nearest-neighbor-Gaussian-Processes.Rmd’
--- re-building ‘Standard-Gaussian-Processes.Rmd’ using rmarkdown
2025-12-21 13:25:37.52922 gimli1 1275701 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Standard-Gaussian-Processes.Rmd:83-93 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Standard-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘Standard-Gaussian-Processes.Rmd’
SUMMARY: processing the following files failed:
‘GPCERF.Rmd’ ‘Nearest-neighbor-Gaussian-Processes.Rmd’
‘Standard-Gaussian-Processes.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [146s/479s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-21 17:14:03.923455 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Saving _problems/test-compute_deriv_nn-21.R
2025-12-21 17:14:20.375395 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_deriv_weights_gp-17.R
2025-12-21 17:14:38.571093 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_m_sigma-32.R
2025-12-21 17:15:01.8909 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:15:18.311083 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:15:32.989228 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=3999837 on localhost:11521 at 17:15:34.241
2025-12-21 17:15:44.512754 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 11.523 s.
2025-12-21 17:15:44.703194 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:15:53.88295 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:16:06.317196 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_weight_gp-49.R
2025-12-21 17:16:19.891044 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:16:30.486801 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:16:43.122546 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:16:53.05197 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:16:53.132591 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:17:09.849059 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:17:09.904713 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:17:09.960141 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:17:10.015242 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:17:10.084562 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:17:10.150124 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:17:10.22412 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:17:10.324969 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:17:27.057343 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
starting worker pid=4014920 on localhost:11521 at 17:17:28.092
starting worker pid=4014919 on localhost:11521 at 17:17:28.297
2025-12-21 17:17:59.84917 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:18:18.806262 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:18:19.26263 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-21 17:18:19.271837 gannet.stats.ox.ac.uk 3986278 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=4019974 on localhost:11521 at 17:18:20.777
2025-12-21 17:18:37.610634 gannet.stats.ox.ac.uk 3986278 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 18.335 s.} ...
2025-12-21 17:18:37.621314 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=4021432 on localhost:11521 at 17:18:39.435
2025-12-21 17:18:54.511929 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 16.89 s.
2025-12-21 17:18:54.520722 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=4023001 on localhost:11521 at 17:18:55.353
2025-12-21 17:19:12.730582 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 18.21 s.
2025-12-21 17:19:12.738789 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 53.476 s.
2025-12-21 17:19:12.761729 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:19:12.804733 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-21 17:19:12.887784 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:19:12.920211 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-21 17:19:13.093878 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:19:13.334097 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-21 17:19:14.011354 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:19:23.545686 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:19:23.613 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-21 17:19:23.669314 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:19:23.70406 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-21 17:19:23.838045 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-estimate_gps-15.R
2025-12-21 17:19:36.364128 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:19:51.67213 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=4028861 on localhost:11521 at 17:19:52.688
2025-12-21 17:20:09.452617 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 17.78 s.
2025-12-21 17:20:09.46382 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=4030898 on localhost:11521 at 17:20:10.040
2025-12-21 17:20:24.238665 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 14.775 s.
Saving _problems/test-estimate_mean_sd_nn-37.R
2025-12-21 17:20:24.413669 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:20:35.795772 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:20:50.365597 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=4035673 on localhost:11521 at 17:20:51.166
2025-12-21 17:21:05.243493 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 14.878 s.
2025-12-21 17:21:05.412154 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:21:22.098838 gannet.stats.ox.ac.uk 3986278 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=4039037 on localhost:11521 at 17:21:22.972
2025-12-21 17:21:42.425644 gannet.stats.ox.ac.uk 3986278 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 20.319 s.} ...
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-compute_deriv_nn.R:21:3'): compute_deriv_nn works as expected! ──
Expected `deriv_val[1, 1]` to equal 1.558466.
Differences:
`actual`: -1.0
`expected`: 1.6
── Failure ('test-compute_deriv_weights_gp.R:17:3'): compute_deriv_weights_gp works as expected! ──
Expected `weights[37]` to equal 3.307249e-05.
Differences:
`actual`: -0.00011
`expected`: 0.00003
── Failure ('test-compute_m_sigma.R:32:4'): compute_m_sigma works as expected! ──
Expected `gp_cerf[10]` to equal 2.105425.
Differences:
`actual`: -6.1
`expected`: 2.1
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Failure ('test-estimate_gps.R:15:3'): estimate_gps works as expected. ───────
Expected `gps_m$gps[4, 1]` to equal 8.74310154.
Differences:
`actual`: 7.3
`expected`: 8.7
── Failure ('test-estimate_mean_sd_nn.R:37:3'): estimate_mean_sd_nn works as expected! ──
Expected `val[10]` to equal 5.031225.
Differences:
`actual`: 5.067
`expected`: 5.031
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [41s/114s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-11 21:32:34.287469 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_nn-8.R
2025-12-11 21:32:40.824217 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_weights_gp-8.R
2025-12-11 21:32:45.521573 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_m_sigma-12.R
2025-12-11 21:32:49.74456 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_m_nn-10.R
2025-12-11 21:32:55.928968 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_sd_nn-10.R
2025-12-11 21:33:04.097866 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_gp-8.R
2025-12-11 21:33:09.241083 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_nn-8.R
2025-12-11 21:33:14.136428 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_sd_gp-17.R
Saving _problems/test-compute_weight_gp-49.R
2025-12-11 21:33:24.304782 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_gp-10.R
2025-12-11 21:33:29.268255 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_nngp-10.R
2025-12-11 21:33:34.101831 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_gps-10.R
2025-12-11 21:33:39.656175 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_mean_sd_nn-10.R
2025-12-11 21:33:44.826404 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_gp-11.R
2025-12-11 21:33:49.354327 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_nn-10.R
2025-12-11 21:33:55.268609 gannet.stats.ox.ac.uk 208070 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-find_optimal_nn-9.R
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compute_deriv_nn.R:5:3'): compute_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_deriv_weights_gp.R:5:3'): compute_deriv_weights_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_weights_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_m_sigma.R:9:4'): compute_m_sigma works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_m_sigma.R:9:4
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_m_nn.R:7:3'): compute_posterior_m_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_m_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_sd_nn.R:7:3'): compute_posterior_sd_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_gp.R:5:3'): compute_rl_deriv_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_nn.R:5:3'): compute_rl_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_sd_gp.R:14:4'): compute_sd_gp works as expected. ───────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_sd_gp.R:14:4
2. └─SuperLearner::SuperLearner(...)
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Error ('test-estimate_cerf_gp.R:7:3'): estimate_cerf_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_gp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_cerf_nngp.R:7:3'): estimate_cerf_nngp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_nngp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_gps.R:7:3'): estimate_gps works as expected. ──────────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_gps.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_mean_sd_nn.R:7:3'): estimate_mean_sd_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_mean_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_gp.R:8:3'): estimate_noise_gp works as expected ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_gp.R:8:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_nn.R:7:3'): estimate_noise_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-find_optimal_nn.R:6:3'): find_optimal_nn works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-find_optimal_nn.R:6:3
2. └─SuperLearner::SuperLearner(...)
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘A-Note-on-Choosing-Hyperparameters.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘A-Note-on-Choosing-Hyperparameters.Rmd’
--- re-building ‘Developers-Guide.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Developers-Guide.Rmd’
--- re-building ‘GPCERF.Rmd’ using rmarkdown
2025-12-11 21:35:45.752456 gannet.stats.ox.ac.uk 221479 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from GPCERF.Rmd:38-45 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GPCERF.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘GPCERF.Rmd’
--- re-building ‘Nearest-neighbor-Gaussian-Processes.Rmd’ using rmarkdown
2025-12-11 21:36:41.197524 gannet.stats.ox.ac.uk 223336 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Nearest-neighbor-Gaussian-Processes.Rmd:83-92 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Nearest-neighbor-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘Nearest-neighbor-Gaussian-Processes.Rmd’
--- re-building ‘Standard-Gaussian-Processes.Rmd’ using rmarkdown
2025-12-11 21:37:28.355464 gannet.stats.ox.ac.uk 229011 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Standard-Gaussian-Processes.Rmd:83-93 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Standard-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘Standard-Gaussian-Processes.Rmd’
SUMMARY: processing the following files failed:
‘GPCERF.Rmd’ ‘Nearest-neighbor-Gaussian-Processes.Rmd’
‘Standard-Gaussian-Processes.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2.4
Check: tests
Result: ERROR
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-17 09:17:49.821386 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_nn-8.R
2025-12-17 09:17:51.096294 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_weights_gp-8.R
2025-12-17 09:17:51.929742 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_m_sigma-12.R
2025-12-17 09:17:52.750785 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_m_nn-10.R
2025-12-17 09:17:53.536041 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_sd_nn-10.R
2025-12-17 09:17:54.475887 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_gp-8.R
2025-12-17 09:17:55.223739 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_nn-8.R
2025-12-17 09:17:56.004034 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_sd_gp-17.R
Saving _problems/test-compute_weight_gp-49.R
2025-12-17 09:17:57.230403 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_gp-10.R
2025-12-17 09:17:58.024499 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_nngp-10.R
2025-12-17 09:17:58.827859 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_gps-10.R
2025-12-17 09:17:59.625059 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_mean_sd_nn-10.R
2025-12-17 09:18:00.363278 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_gp-11.R
2025-12-17 09:18:01.151327 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_nn-10.R
2025-12-17 09:18:01.983663 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-find_optimal_nn-9.R
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compute_deriv_nn.R:5:3'): compute_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_deriv_weights_gp.R:5:3'): compute_deriv_weights_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_weights_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_m_sigma.R:9:4'): compute_m_sigma works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_m_sigma.R:9:4
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_m_nn.R:7:3'): compute_posterior_m_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_m_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_sd_nn.R:7:3'): compute_posterior_sd_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_gp.R:5:3'): compute_rl_deriv_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_nn.R:5:3'): compute_rl_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_sd_gp.R:14:4'): compute_sd_gp works as expected. ───────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_sd_gp.R:14:4
2. └─SuperLearner::SuperLearner(...)
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Error ('test-estimate_cerf_gp.R:7:3'): estimate_cerf_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_gp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_cerf_nngp.R:7:3'): estimate_cerf_nngp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_nngp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_gps.R:7:3'): estimate_gps works as expected. ──────────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_gps.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_mean_sd_nn.R:7:3'): estimate_mean_sd_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_mean_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_gp.R:8:3'): estimate_noise_gp works as expected ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_gp.R:8:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_nn.R:7:3'): estimate_noise_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-find_optimal_nn.R:6:3'): find_optimal_nn works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-find_optimal_nn.R:6:3
2. └─SuperLearner::SuperLearner(...)
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.2.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'A-Note-on-Choosing-Hyperparameters.Rmd' using rmarkdown
--- finished re-building 'A-Note-on-Choosing-Hyperparameters.Rmd'
--- re-building 'Developers-Guide.Rmd' using rmarkdown
--- finished re-building 'Developers-Guide.Rmd'
--- re-building 'GPCERF.Rmd' using rmarkdown
2025-12-17 09:18:12.002599 CRANWIN3 22520 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from GPCERF.Rmd:38-45 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GPCERF.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building 'GPCERF.Rmd'
--- re-building 'Nearest-neighbor-Gaussian-Processes.Rmd' using rmarkdown
2025-12-17 09:18:18.88815 CRANWIN3 17560 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Nearest-neighbor-Gaussian-Processes.Rmd:83-92 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Nearest-neighbor-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building 'Nearest-neighbor-Gaussian-Processes.Rmd'
--- re-building 'Standard-Gaussian-Processes.Rmd' using rmarkdown
2025-12-17 09:18:25.230098 CRANWIN3 17596 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Standard-Gaussian-Processes.Rmd:83-93 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Standard-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building 'Standard-Gaussian-Processes.Rmd'
SUMMARY: processing the following files failed:
'GPCERF.Rmd' 'Nearest-neighbor-Gaussian-Processes.Rmd'
'Standard-Gaussian-Processes.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [27s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-17 05:54:45.971001 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_nn-8.R
2025-12-17 05:54:48.232106 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_weights_gp-8.R
2025-12-17 05:54:50.31752 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_m_sigma-12.R
2025-12-17 05:54:52.004295 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_m_nn-10.R
2025-12-17 05:54:53.679858 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_sd_nn-10.R
2025-12-17 05:54:55.021348 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_gp-8.R
2025-12-17 05:54:56.416576 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_nn-8.R
2025-12-17 05:54:58.385254 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_sd_gp-17.R
Saving _problems/test-compute_weight_gp-49.R
2025-12-17 05:55:03.527437 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_gp-10.R
2025-12-17 05:55:05.353983 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_nngp-10.R
2025-12-17 05:55:06.787716 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_gps-10.R
2025-12-17 05:55:08.519506 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_mean_sd_nn-10.R
2025-12-17 05:55:10.32453 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_gp-11.R
2025-12-17 05:55:12.3509 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_nn-10.R
2025-12-17 05:55:14.213034 gimli2 2175925 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-find_optimal_nn-9.R
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compute_deriv_nn.R:5:3'): compute_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_deriv_weights_gp.R:5:3'): compute_deriv_weights_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_weights_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_m_sigma.R:9:4'): compute_m_sigma works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_m_sigma.R:9:4
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_m_nn.R:7:3'): compute_posterior_m_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_m_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_sd_nn.R:7:3'): compute_posterior_sd_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_gp.R:5:3'): compute_rl_deriv_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_nn.R:5:3'): compute_rl_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_sd_gp.R:14:4'): compute_sd_gp works as expected. ───────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_sd_gp.R:14:4
2. └─SuperLearner::SuperLearner(...)
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Error ('test-estimate_cerf_gp.R:7:3'): estimate_cerf_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_gp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_cerf_nngp.R:7:3'): estimate_cerf_nngp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_nngp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_gps.R:7:3'): estimate_gps works as expected. ──────────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_gps.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_mean_sd_nn.R:7:3'): estimate_mean_sd_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_mean_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_gp.R:8:3'): estimate_noise_gp works as expected ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_gp.R:8:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_nn.R:7:3'): estimate_noise_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-find_optimal_nn.R:6:3'): find_optimal_nn works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-find_optimal_nn.R:6:3
2. └─SuperLearner::SuperLearner(...)
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
Error:
! Test failures.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.2.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘A-Note-on-Choosing-Hyperparameters.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘A-Note-on-Choosing-Hyperparameters.Rmd’
--- re-building ‘Developers-Guide.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Developers-Guide.Rmd’
--- re-building ‘GPCERF.Rmd’ using rmarkdown
2025-12-17 05:55:29.959503 gimli2 2190048 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from GPCERF.Rmd:38-45 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GPCERF.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘GPCERF.Rmd’
--- re-building ‘Nearest-neighbor-Gaussian-Processes.Rmd’ using rmarkdown
2025-12-17 05:55:42.593611 gimli2 2191307 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Nearest-neighbor-Gaussian-Processes.Rmd:83-92 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Nearest-neighbor-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘Nearest-neighbor-Gaussian-Processes.Rmd’
--- re-building ‘Standard-Gaussian-Processes.Rmd’ using rmarkdown
2025-12-17 05:55:53.665771 gimli2 2194180 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Standard-Gaussian-Processes.Rmd:83-93 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Standard-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘Standard-Gaussian-Processes.Rmd’
SUMMARY: processing the following files failed:
‘GPCERF.Rmd’ ‘Nearest-neighbor-Gaussian-Processes.Rmd’
‘Standard-Gaussian-Processes.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [27s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-13 05:44:57.923033 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_nn-8.R
2025-12-13 05:45:00.416523 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_weights_gp-8.R
2025-12-13 05:45:01.93277 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_m_sigma-12.R
2025-12-13 05:45:03.526912 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_m_nn-10.R
2025-12-13 05:45:05.100099 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_sd_nn-10.R
2025-12-13 05:45:06.917073 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_gp-8.R
2025-12-13 05:45:08.314523 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_nn-8.R
2025-12-13 05:45:09.767577 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_sd_gp-17.R
Saving _problems/test-compute_weight_gp-49.R
2025-12-13 05:45:13.986624 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_gp-10.R
2025-12-13 05:45:15.681828 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_nngp-10.R
2025-12-13 05:45:17.029967 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_gps-10.R
2025-12-13 05:45:18.675501 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_mean_sd_nn-10.R
2025-12-13 05:45:20.369581 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_gp-11.R
2025-12-13 05:45:22.178111 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_nn-10.R
2025-12-13 05:45:24.016171 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-find_optimal_nn-9.R
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compute_deriv_nn.R:5:3'): compute_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_deriv_weights_gp.R:5:3'): compute_deriv_weights_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_weights_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_m_sigma.R:9:4'): compute_m_sigma works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_m_sigma.R:9:4
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_m_nn.R:7:3'): compute_posterior_m_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_m_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_sd_nn.R:7:3'): compute_posterior_sd_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_gp.R:5:3'): compute_rl_deriv_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_nn.R:5:3'): compute_rl_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_sd_gp.R:14:4'): compute_sd_gp works as expected. ───────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_sd_gp.R:14:4
2. └─SuperLearner::SuperLearner(...)
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Error ('test-estimate_cerf_gp.R:7:3'): estimate_cerf_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_gp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_cerf_nngp.R:7:3'): estimate_cerf_nngp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_nngp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_gps.R:7:3'): estimate_gps works as expected. ──────────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_gps.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_mean_sd_nn.R:7:3'): estimate_mean_sd_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_mean_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_gp.R:8:3'): estimate_noise_gp works as expected ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_gp.R:8:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_nn.R:7:3'): estimate_noise_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-find_optimal_nn.R:6:3'): find_optimal_nn works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-find_optimal_nn.R:6:3
2. └─SuperLearner::SuperLearner(...)
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.2.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘A-Note-on-Choosing-Hyperparameters.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘A-Note-on-Choosing-Hyperparameters.Rmd’
--- re-building ‘Developers-Guide.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Developers-Guide.Rmd’
--- re-building ‘GPCERF.Rmd’ using rmarkdown
2025-12-13 05:45:38.029637 gimli2 274017 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from GPCERF.Rmd:38-45 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GPCERF.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘GPCERF.Rmd’
--- re-building ‘Nearest-neighbor-Gaussian-Processes.Rmd’ using rmarkdown
2025-12-13 05:45:48.80051 gimli2 275346 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Nearest-neighbor-Gaussian-Processes.Rmd:83-92 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Nearest-neighbor-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘Nearest-neighbor-Gaussian-Processes.Rmd’
--- re-building ‘Standard-Gaussian-Processes.Rmd’ using rmarkdown
2025-12-13 05:45:58.960181 gimli2 277514 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Standard-Gaussian-Processes.Rmd:83-93 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Standard-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘Standard-Gaussian-Processes.Rmd’
SUMMARY: processing the following files failed:
‘GPCERF.Rmd’ ‘Nearest-neighbor-Gaussian-Processes.Rmd’
‘Standard-Gaussian-Processes.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.2.4
Check: tests
Result: ERROR
Running 'testthat.R' [23s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-19 07:36:30.227615 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_nn-8.R
2025-12-19 07:36:31.543588 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_weights_gp-8.R
2025-12-19 07:36:32.978871 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_m_sigma-12.R
2025-12-19 07:36:34.062103 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_m_nn-10.R
2025-12-19 07:36:34.943632 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_sd_nn-10.R
2025-12-19 07:36:36.109486 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_gp-8.R
2025-12-19 07:36:37.198997 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_nn-8.R
2025-12-19 07:36:38.215173 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_sd_gp-17.R
Saving _problems/test-compute_weight_gp-49.R
2025-12-19 07:36:39.837966 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_gp-10.R
2025-12-19 07:36:40.916916 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_nngp-10.R
2025-12-19 07:36:42.067341 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_gps-10.R
2025-12-19 07:36:43.122727 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_mean_sd_nn-10.R
2025-12-19 07:36:44.562531 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_gp-11.R
2025-12-19 07:36:45.618777 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_nn-10.R
2025-12-19 07:36:46.854575 CRANWIN2 86912 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-find_optimal_nn-9.R
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compute_deriv_nn.R:5:3'): compute_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_deriv_weights_gp.R:5:3'): compute_deriv_weights_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_weights_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_m_sigma.R:9:4'): compute_m_sigma works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_m_sigma.R:9:4
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_m_nn.R:7:3'): compute_posterior_m_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_m_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_sd_nn.R:7:3'): compute_posterior_sd_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_gp.R:5:3'): compute_rl_deriv_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_nn.R:5:3'): compute_rl_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_sd_gp.R:14:4'): compute_sd_gp works as expected. ───────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_sd_gp.R:14:4
2. └─SuperLearner::SuperLearner(...)
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Error ('test-estimate_cerf_gp.R:7:3'): estimate_cerf_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_gp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_cerf_nngp.R:7:3'): estimate_cerf_nngp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_nngp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_gps.R:7:3'): estimate_gps works as expected. ──────────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_gps.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_mean_sd_nn.R:7:3'): estimate_mean_sd_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_mean_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_gp.R:8:3'): estimate_noise_gp works as expected ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_gp.R:8:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_nn.R:7:3'): estimate_noise_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-find_optimal_nn.R:6:3'): find_optimal_nn works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-find_optimal_nn.R:6:3
2. └─SuperLearner::SuperLearner(...)
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 0.2.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'A-Note-on-Choosing-Hyperparameters.Rmd' using rmarkdown
--- finished re-building 'A-Note-on-Choosing-Hyperparameters.Rmd'
--- re-building 'Developers-Guide.Rmd' using rmarkdown
--- finished re-building 'Developers-Guide.Rmd'
--- re-building 'GPCERF.Rmd' using rmarkdown
2025-12-19 07:36:59.709948 CRANWIN2 103056 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from GPCERF.Rmd:38-45 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GPCERF.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building 'GPCERF.Rmd'
--- re-building 'Nearest-neighbor-Gaussian-Processes.Rmd' using rmarkdown
2025-12-19 07:37:10.116487 CRANWIN2 23580 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Nearest-neighbor-Gaussian-Processes.Rmd:83-92 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Nearest-neighbor-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building 'Nearest-neighbor-Gaussian-Processes.Rmd'
--- re-building 'Standard-Gaussian-Processes.Rmd' using rmarkdown
2025-12-19 07:37:19.186744 CRANWIN2 27140 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Standard-Gaussian-Processes.Rmd:83-93 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Standard-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building 'Standard-Gaussian-Processes.Rmd'
SUMMARY: processing the following files failed:
'GPCERF.Rmd' 'Nearest-neighbor-Gaussian-Processes.Rmd'
'Standard-Gaussian-Processes.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-x86_64