* using log directory ‘/data/gannet/ripley/R/packages/tests-gcc-SAN/GPCERF.Rcheck’ * using R Under development (unstable) (2025-12-05 r89105) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2) GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘GPCERF/DESCRIPTION’ ... OK * this is package ‘GPCERF’ version ‘0.2.4’ * package encoding: UTF-8 * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package ‘GPCERF’ can be installed ... [102s/96s] WARNING Found the following significant warnings: /data/gannet/ripley/R/gcc-SAN3/include/R_ext/Callbacks.h:32:2: warning: ‘#warning’ before C++23 is a GCC extension [-Wc++23-extensions] See ‘/data/gannet/ripley/R/packages/tests-gcc-SAN/GPCERF.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ * checking C++ specification ... OK * checking package directory ... OK * checking whether the package can be loaded ... [12s/12s] OK * checking whether the package can be loaded with stated dependencies ... [10s/10s] OK * checking whether the package can be unloaded cleanly ... [11s/11s] OK * checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK * checking whether the namespace can be unloaded cleanly ... [12s/12s] OK * checking loading without being on the library search path ... [11s/11s] OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [12s/12s] OK * checking tests ... [79s/80s] ERROR Running ‘testthat.R’ [78s/79s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(GPCERF) > > test_check("GPCERF") 2025-12-05 13:22:45.647404 gannet.stats.ox.ac.uk 791971 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 2025-12-05 13:22:50.555276 gannet.stats.ox.ac.uk 791971 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 2025-12-05 13:22:54.766001 gannet.stats.ox.ac.uk 791971 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 2025-12-05 13:22:58.63708 gannet.stats.ox.ac.uk 791971 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 2025-12-05 13:23:02.507226 gannet.stats.ox.ac.uk 791971 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 2025-12-05 13:23:06.440736 gannet.stats.ox.ac.uk 791971 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 2025-12-05 13:23:10.213593 gannet.stats.ox.ac.uk 791971 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 2025-12-05 13:23:14.01578 gannet.stats.ox.ac.uk 791971 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 2025-12-05 13:23:19.11976 gannet.stats.ox.ac.uk 791971 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 2025-12-05 13:23:22.952282 gannet.stats.ox.ac.uk 791971 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 2025-12-05 13:23:26.776662 gannet.stats.ox.ac.uk 791971 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 2025-12-05 13:23:30.596582 gannet.stats.ox.ac.uk 791971 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 2025-12-05 13:23:34.436121 gannet.stats.ox.ac.uk 791971 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 2025-12-05 13:23:38.797978 gannet.stats.ox.ac.uk 791971 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 2025-12-05 13:23:42.848513 gannet.stats.ox.ac.uk 791971 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 * checking package vignettes ... OK * checking re-building of vignette outputs ... [107s/108s] 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 2025-12-05 13:24:40.906517 gannet.stats.ox.ac.uk 794240 GPCERF estimate_gps INFO: Started estimating GPS values ... Quitting from GPCERF.Rmd:38-45 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 2025-12-05 13:25:12.082137 gannet.stats.ox.ac.uk 794304 GPCERF estimate_gps INFO: Started estimating GPS values ... Quitting from Nearest-neighbor-Gaussian-Processes.Rmd:83-92 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 2025-12-05 13:25:39.421622 gannet.stats.ox.ac.uk 795120 GPCERF estimate_gps INFO: Started estimating GPS values ... Quitting from Standard-Gaussian-Processes.Rmd:83-93 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 * DONE Status: 2 ERRORs, 1 WARNING