CRAN Package Check Results for Maintainer ‘Boyu Ren <bren at mgb.org>’

Last updated on 2025-12-04 09:50:18 CET.

Package	ERROR	NOTE	OK
GPCERF	2	2	9

Package GPCERF

Current CRAN status: ERROR: 2, NOTE: 2, OK: 9

Additional issues

donttest

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