* using log directory ‘/data/gannet/ripley/R/packages/tests-MKL/GPCERF.Rcheck’ * using R Under development (unstable) (2025-12-30 r89257) * 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 namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘GPCERF’ can be installed ... [26s/27s] OK * used C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [18s/18s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [82s/116s] [82s/116s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(GPCERF) > > test_check("GPCERF") 2025-12-30 10:47:11.873138 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... Loading required package: nnls Saving _problems/test-compute_deriv_nn-21.R 2025-12-30 10:47:16.18915 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... Saving _problems/test-compute_deriv_weights_gp-17.R 2025-12-30 10:47:20.142405 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... Saving _problems/test-compute_m_sigma-32.R 2025-12-30 10:47:27.512715 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... 2025-12-30 10:47:31.187776 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... 2025-12-30 10:47:34.913757 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ... starting worker pid=1484212 on localhost:11927 at 10:47:35.176 2025-12-30 10:47:38.418432 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.504 s. 2025-12-30 10:47:38.482106 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... 2025-12-30 10:47:42.119002 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... 2025-12-30 10:47:45.83695 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... Saving _problems/test-compute_weight_gp-49.R 2025-12-30 10:47:49.637448 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... 2025-12-30 10:47:53.219745 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:47:56.769309 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... 2025-12-30 10:47:59.457869 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:47:59.494378 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... 2025-12-30 10:48:03.4084 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:48:03.425519 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:48:03.456199 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:48:03.47375 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:48:03.490893 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:48:03.518105 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:48:03.546101 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:48:03.565935 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... 2025-12-30 10:48:07.226643 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 starting worker pid=1485288 on localhost:11927 at 10:48:07.515 starting worker pid=1485289 on localhost:11927 at 10:48:07.591 2025-12-30 10:48:14.555618 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... 2025-12-30 10:48:18.254872 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:48:18.278495 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ... 2025-12-30 10:48:18.285921 gannet.stats.ox.ac.uk 1481848 GPCERF find_optimal_nn INFO: Started finding optimal values ... starting worker pid=1485625 on localhost:11927 at 10:48:18.536 2025-12-30 10:48:21.861418 gannet.stats.ox.ac.uk 1481848 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 3.572 s.} ... 2025-12-30 10:48:21.865045 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ... starting worker pid=1485730 on localhost:11927 at 10:48:22.116 2025-12-30 10:48:24.984048 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.119 s. 2025-12-30 10:48:24.987585 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ... starting worker pid=1485771 on localhost:11927 at 10:48:25.237 2025-12-30 10:48:29.301499 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 4.313 s. 2025-12-30 10:48:29.305012 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 11.027 s. 2025-12-30 10:48:29.311469 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:48:29.320538 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ... 2025-12-30 10:48:29.343725 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:48:29.352738 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ... 2025-12-30 10:48:29.39193 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:48:29.401639 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ... 2025-12-30 10:48:29.421458 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... 2025-12-30 10:48:31.98743 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:48:31.995679 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ... 2025-12-30 10:48:32.010072 gannet.stats.ox.ac.uk 1481848 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-30 r89257), detected cores: 24 2025-12-30 10:48:32.019041 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ... 2025-12-30 10:48:32.058843 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... Saving _problems/test-estimate_gps-15.R 2025-12-30 10:48:35.671311 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... 2025-12-30 10:48:39.296099 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ... starting worker pid=1486215 on localhost:11927 at 10:48:39.543 2025-12-30 10:48:42.398034 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.102 s. 2025-12-30 10:48:42.401958 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ... starting worker pid=1486509 on localhost:11927 at 10:48:42.696 2025-12-30 10:48:46.284657 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 3.88300000000001 s. Saving _problems/test-estimate_mean_sd_nn-37.R 2025-12-30 10:48:46.358563 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... 2025-12-30 10:48:48.933897 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... 2025-12-30 10:48:52.58815 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ... starting worker pid=1486925 on localhost:11927 at 10:48:52.846 2025-12-30 10:48:55.870965 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.283 s. 2025-12-30 10:48:55.900536 gannet.stats.ox.ac.uk 1481848 GPCERF estimate_gps INFO: Started estimating GPS values ... 2025-12-30 10:48:59.664324 gannet.stats.ox.ac.uk 1481848 GPCERF find_optimal_nn INFO: Started finding optimal values ... starting worker pid=1487471 on localhost:11927 at 10:48:59.917 2025-12-30 10:49:03.984617 gannet.stats.ox.ac.uk 1481848 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 4.318 s.} ... [ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-compute_deriv_nn.R:21:3'): compute_deriv_nn works as expected! ── Expected `deriv_val[1, 1]` to equal 1.558466. Differences: `actual`: -1.0 `expected`: 1.6 ── Failure ('test-compute_deriv_weights_gp.R:17:3'): compute_deriv_weights_gp works as expected! ── Expected `weights[37]` to equal 3.307249e-05. Differences: `actual`: -0.00011 `expected`: 0.00003 ── Failure ('test-compute_m_sigma.R:32:4'): compute_m_sigma works as expected! ── Expected `gp_cerf[10]` to equal 2.105425. Differences: `actual`: -6.1 `expected`: 2.1 ── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ───────────── Expected `weight$weight[28]` to equal 0.0002182767. Differences: `actual`: 0.00000 `expected`: 0.00022 ── Failure ('test-estimate_gps.R:15:3'): estimate_gps works as expected. ─────── Expected `gps_m$gps[4, 1]` to equal 8.74310154. Differences: `actual`: 7.3 `expected`: 8.7 ── Failure ('test-estimate_mean_sd_nn.R:37:3'): estimate_mean_sd_nn works as expected! ── Expected `val[10]` to equal 5.031225. Differences: `actual`: 5.067 `expected`: 5.031 [ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [85s/126s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/gannet/ripley/R/packages/tests-MKL/GPCERF.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 6:11.43, 271.08 + 22.97