Last updated on 2025-12-05 01:49:01 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.4 | 31.17 | 443.61 | 474.78 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.2.4 | 17.48 | 269.95 | 287.43 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.2.4 | 117.00 | 206.70 | 323.70 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.4 | 202.00 | 121.84 | 323.84 | ERROR | |
| r-devel-windows-x86_64 | 0.2.4 | 36.00 | 470.00 | 506.00 | OK | |
| r-patched-linux-x86_64 | 0.2.4 | 27.44 | 350.41 | 377.85 | OK | |
| r-release-linux-x86_64 | 0.2.4 | 28.40 | 350.68 | 379.08 | OK | |
| r-release-macos-arm64 | 0.2.4 | OK | ||||
| r-release-macos-x86_64 | 0.2.4 | 22.00 | 418.00 | 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 | 32.00 | 365.00 | 397.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.4 | 45.00 | 665.00 | 710.00 | OK |
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’ [48s/120s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-03 10:46:21.230048 gannet.stats.ox.ac.uk 2774151 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
2025-12-03 10:46:29.802748 gannet.stats.ox.ac.uk 2774151 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
2025-12-03 10:46:36.945569 gannet.stats.ox.ac.uk 2774151 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
2025-12-03 10:46:43.126978 gannet.stats.ox.ac.uk 2774151 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
2025-12-03 10:46:47.58651 gannet.stats.ox.ac.uk 2774151 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
2025-12-03 10:46:53.405592 gannet.stats.ox.ac.uk 2774151 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
2025-12-03 10:46:58.661949 gannet.stats.ox.ac.uk 2774151 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
2025-12-03 10:47:04.573063 gannet.stats.ox.ac.uk 2774151 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
2025-12-03 10:47:11.939263 gannet.stats.ox.ac.uk 2774151 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
2025-12-03 10:47:18.331096 gannet.stats.ox.ac.uk 2774151 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
2025-12-03 10:47:22.500888 gannet.stats.ox.ac.uk 2774151 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
2025-12-03 10:47:28.994736 gannet.stats.ox.ac.uk 2774151 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
2025-12-03 10:47:36.311445 gannet.stats.ox.ac.uk 2774151 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
2025-12-03 10:47:42.712992 gannet.stats.ox.ac.uk 2774151 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
2025-12-03 10:47:46.154439 gannet.stats.ox.ac.uk 2774151 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-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
2025-12-03 10:48:45.642728 gannet.stats.ox.ac.uk 2791218 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
2025-12-03 10:49:30.72849 gannet.stats.ox.ac.uk 2793348 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
2025-12-03 10:50:14.34874 gannet.stats.ox.ac.uk 2803855 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-clang
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [40s/142s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-03 11:31:13.427045 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:31:24.319803 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:31:34.72926 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:31:44.582719 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:31:52.302332 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:32:02.896598 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:32:10.000469 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:32:13.992651 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:32:21.95571 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:32:28.036271 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:32:35.021695 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:32:41.798034 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:32:47.426036 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:32:53.265801 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:32:59.008773 gannet.stats.ox.ac.uk 3075126 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
2025-12-03 11:35:19.711104 gannet.stats.ox.ac.uk 3095964 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
2025-12-03 11:36:19.746477 gannet.stats.ox.ac.uk 3099533 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
2025-12-03 11:37:18.623246 gannet.stats.ox.ac.uk 3105429 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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.