Last updated on 2025-12-25 19:50:15 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.4 | 27.52 | 338.06 | 365.58 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2.4 | 17.12 | 211.42 | 228.54 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.4 | 61.00 | 451.40 | 512.40 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.4 | 49.00 | 454.36 | 503.36 | ERROR | |
| r-devel-windows-x86_64 | 0.2.4 | 35.00 | 164.00 | 199.00 | ERROR | |
| r-patched-linux-x86_64 | 0.2.4 | 28.17 | 260.51 | 288.68 | ERROR | |
| r-release-linux-x86_64 | 0.2.4 | 25.96 | 146.59 | 172.55 | ERROR | |
| r-release-macos-arm64 | 0.2.4 | OK | ||||
| r-release-macos-x86_64 | 0.2.4 | 17.00 | 423.00 | 440.00 | OK | |
| r-release-windows-x86_64 | 0.2.4 | 36.00 | 385.00 | 421.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.2.4 | OK | ||||
| r-oldrel-macos-x86_64 | 0.2.4 | 20.00 | 377.00 | 397.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.4 | 42.00 | 554.00 | 596.00 | ERROR |
Version: 0.2.4
Check: DESCRIPTION meta-information
Result: NOTE
Author field differs from that derived from Authors@R
Author: ‘Naeem Khoshnevis [aut] (<https://orcid.org/0000-0003-4315-1426>, HUIT), Boyu Ren [aut, cre] (<https://orcid.org/0000-0002-5300-1184>, McLean Hospital), Tanujit Dey [ctb] (<https://orcid.org/0000-0001-5559-211X>, HMS), Danielle Braun [aut] (<https://orcid.org/0000-0002-5177-8598>, HSPH)’
Authors@R: ‘Naeem Khoshnevis [aut] (ORCID: <https://orcid.org/0000-0003-4315-1426>, AFFILIATION: HUIT), Boyu Ren [aut, cre] (ORCID: <https://orcid.org/0000-0002-5300-1184>, AFFILIATION: McLean Hospital), Tanujit Dey [ctb] (ORCID: <https://orcid.org/0000-0001-5559-211X>, AFFILIATION: HMS), Danielle Braun [aut] (ORCID: <https://orcid.org/0000-0002-5177-8598>, AFFILIATION: HSPH)’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [131s/134s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-22 17:35:29.829303 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Saving _problems/test-compute_deriv_nn-21.R
2025-12-22 17:35:34.109678 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_deriv_weights_gp-17.R
2025-12-22 17:35:37.790682 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_m_sigma-32.R
2025-12-22 17:35:44.299954 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 17:35:47.908548 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 17:35:51.436641 gimli2 1827049 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=1834231 on localhost:11582 at 17:35:51.865
2025-12-22 17:35:55.585659 gimli2 1827049 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 4.149 s.
2025-12-22 17:35:55.681507 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 17:35:59.16841 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 17:36:02.737651 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_weight_gp-49.R
2025-12-22 17:36:06.961057 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 17:36:10.565609 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:13.585728 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 17:36:16.085748 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:16.114923 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 17:36:19.824885 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:19.860352 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:19.903113 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:19.939092 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:19.968078 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:20.00903 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:20.055442 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:20.09087 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 17:36:23.905115 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
starting worker pid=1841248 on localhost:11582 at 17:36:24.314
starting worker pid=1841249 on localhost:11582 at 17:36:24.349
2025-12-22 17:36:33.655403 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 17:36:37.149608 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:37.161491 gimli2 1827049 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-22 17:36:37.170325 gimli2 1827049 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=1845450 on localhost:11582 at 17:36:37.616
2025-12-22 17:36:42.348456 gimli2 1827049 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 5.176 s.} ...
2025-12-22 17:36:42.350995 gimli2 1827049 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=1846668 on localhost:11582 at 17:36:42.801
2025-12-22 17:36:49.093406 gimli2 1827049 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 6.74299999999999 s.
2025-12-22 17:36:49.096303 gimli2 1827049 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=1849219 on localhost:11582 at 17:36:49.546
2025-12-22 17:36:55.375616 gimli2 1827049 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 6.279 s.
2025-12-22 17:36:55.37798 gimli2 1827049 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 18.216 s.
2025-12-22 17:36:55.386687 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:55.395161 gimli2 1827049 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-22 17:36:55.421263 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:55.431014 gimli2 1827049 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-22 17:36:55.502662 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:55.515468 gimli2 1827049 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-22 17:36:55.538712 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 17:36:57.87326 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:57.88891 gimli2 1827049 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-22 17:36:57.903723 gimli2 1827049 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-21 r89216), detected cores: 32
2025-12-22 17:36:57.919029 gimli2 1827049 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-22 17:36:57.977055 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-estimate_gps-15.R
2025-12-22 17:37:01.726438 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 17:37:05.319479 gimli2 1827049 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=1853528 on localhost:11582 at 17:37:05.647
2025-12-22 17:37:10.394426 gimli2 1827049 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 5.075 s.
2025-12-22 17:37:10.39697 gimli2 1827049 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=1854490 on localhost:11582 at 17:37:10.816
2025-12-22 17:37:16.190782 gimli2 1827049 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 5.794 s.
Saving _problems/test-estimate_mean_sd_nn-37.R
2025-12-22 17:37:16.281108 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 17:37:18.723087 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 17:37:22.388053 gimli2 1827049 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=1858166 on localhost:11582 at 17:37:22.873
2025-12-22 17:37:27.680605 gimli2 1827049 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 5.292 s.
2025-12-22 17:37:27.742444 gimli2 1827049 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 17:37:31.796539 gimli2 1827049 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=1860652 on localhost:11582 at 17:37:32.082
2025-12-22 17:37:37.730375 gimli2 1827049 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 5.931 s.} ...
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-compute_deriv_nn.R:21:3'): compute_deriv_nn works as expected! ──
Expected `deriv_val[1, 1]` to equal 1.558466.
Differences:
`actual`: -1.0
`expected`: 1.6
── Failure ('test-compute_deriv_weights_gp.R:17:3'): compute_deriv_weights_gp works as expected! ──
Expected `weights[37]` to equal 3.307249e-05.
Differences:
`actual`: -0.00011
`expected`: 0.00003
── Failure ('test-compute_m_sigma.R:32:4'): compute_m_sigma works as expected! ──
Expected `gp_cerf[10]` to equal 2.105425.
Differences:
`actual`: -6.1
`expected`: 2.1
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Failure ('test-estimate_gps.R:15:3'): estimate_gps works as expected. ───────
Expected `gps_m$gps[4, 1]` to equal 8.74310154.
Differences:
`actual`: 7.3
`expected`: 8.7
── Failure ('test-estimate_mean_sd_nn.R:37:3'): estimate_mean_sd_nn works as expected! ──
Expected `val[10]` to equal 5.031225.
Differences:
`actual`: 5.067
`expected`: 5.031
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [74s/120s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-25 13:23:53.608705 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Saving _problems/test-compute_deriv_nn-21.R
2025-12-25 13:23:59.011287 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_deriv_weights_gp-17.R
2025-12-25 13:24:03.059644 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_m_sigma-32.R
2025-12-25 13:24:09.84639 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-25 13:24:14.042688 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-25 13:24:18.224156 gimli1 904513 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=923332 on localhost:11271 at 13:24:18.610
2025-12-25 13:24:21.316749 gimli1 904513 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.093 s.
2025-12-25 13:24:21.34715 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-25 13:24:25.262491 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-25 13:24:29.206126 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_weight_gp-49.R
2025-12-25 13:24:33.580188 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-25 13:24:37.607455 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:24:40.778116 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-25 13:24:44.246537 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:24:44.282857 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-25 13:24:48.201128 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:24:48.230687 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:24:48.265723 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:24:48.293124 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:24:48.32478 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:24:48.356666 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:24:48.389708 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:24:48.431803 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-25 13:24:52.452386 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
starting worker pid=955646 on localhost:11271 at 13:24:52.896
starting worker pid=955638 on localhost:11271 at 13:24:52.932
2025-12-25 13:24:59.396076 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-25 13:25:02.855176 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:25:02.869335 gimli1 904513 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-25 13:25:02.876803 gimli1 904513 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=964312 on localhost:11271 at 13:25:03.197
2025-12-25 13:25:06.405987 gimli1 904513 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 3.52800000000001 s.} ...
2025-12-25 13:25:06.408081 gimli1 904513 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=966637 on localhost:11271 at 13:25:06.758
2025-12-25 13:25:09.380178 gimli1 904513 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.97200000000001 s.
2025-12-25 13:25:09.382023 gimli1 904513 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=968355 on localhost:11271 at 13:25:09.711
2025-12-25 13:25:14.428795 gimli1 904513 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 5.047 s.
2025-12-25 13:25:14.430549 gimli1 904513 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 11.562 s.
2025-12-25 13:25:14.433692 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:25:14.453457 gimli1 904513 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-25 13:25:14.465316 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:25:14.485186 gimli1 904513 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-25 13:25:14.52648 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:25:14.560227 gimli1 904513 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-25 13:25:14.601213 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-25 13:25:17.570224 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:25:17.585616 gimli1 904513 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-25 13:25:17.601413 gimli1 904513 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R Under development (unstable) (2025-12-24 r89227), detected cores: 64
2025-12-25 13:25:17.617861 gimli1 904513 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-25 13:25:17.658512 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-estimate_gps-15.R
2025-12-25 13:25:21.620566 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-25 13:25:24.757707 gimli1 904513 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=983619 on localhost:11271 at 13:25:25.171
2025-12-25 13:25:27.496161 gimli1 904513 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.738 s.
2025-12-25 13:25:27.498358 gimli1 904513 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=987618 on localhost:11271 at 13:25:27.829
2025-12-25 13:25:31.050453 gimli1 904513 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 3.55199999999999 s.
Saving _problems/test-estimate_mean_sd_nn-37.R
2025-12-25 13:25:31.105474 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-25 13:25:33.92004 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-25 13:25:37.47591 gimli1 904513 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=1001654 on localhost:11271 at 13:25:37.841
2025-12-25 13:25:40.689112 gimli1 904513 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.21300000000001 s.
2025-12-25 13:25:40.73646 gimli1 904513 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-25 13:25:44.48526 gimli1 904513 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=1010213 on localhost:11271 at 13:25:44.870
2025-12-25 13:25:49.288451 gimli1 904513 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 4.801 s.} ...
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-compute_deriv_nn.R:21:3'): compute_deriv_nn works as expected! ──
Expected `deriv_val[1, 1]` to equal 1.558466.
Differences:
`actual`: -1.0
`expected`: 1.6
── Failure ('test-compute_deriv_weights_gp.R:17:3'): compute_deriv_weights_gp works as expected! ──
Expected `weights[37]` to equal 3.307249e-05.
Differences:
`actual`: -0.00011
`expected`: 0.00003
── Failure ('test-compute_m_sigma.R:32:4'): compute_m_sigma works as expected! ──
Expected `gp_cerf[10]` to equal 2.105425.
Differences:
`actual`: -6.1
`expected`: 2.1
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Failure ('test-estimate_gps.R:15:3'): estimate_gps works as expected. ───────
Expected `gps_m$gps[4, 1]` to equal 8.74310154.
Differences:
`actual`: 7.3
`expected`: 8.7
── Failure ('test-estimate_mean_sd_nn.R:37:3'): estimate_mean_sd_nn works as expected! ──
Expected `val[10]` to equal 5.031225.
Differences:
`actual`: 5.067
`expected`: 5.031
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [146s/479s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-21 17:14:03.923455 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Saving _problems/test-compute_deriv_nn-21.R
2025-12-21 17:14:20.375395 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_deriv_weights_gp-17.R
2025-12-21 17:14:38.571093 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_m_sigma-32.R
2025-12-21 17:15:01.8909 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:15:18.311083 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:15:32.989228 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=3999837 on localhost:11521 at 17:15:34.241
2025-12-21 17:15:44.512754 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 11.523 s.
2025-12-21 17:15:44.703194 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:15:53.88295 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:16:06.317196 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_weight_gp-49.R
2025-12-21 17:16:19.891044 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:16:30.486801 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:16:43.122546 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:16:53.05197 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:16:53.132591 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:17:09.849059 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:17:09.904713 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:17:09.960141 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:17:10.015242 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:17:10.084562 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:17:10.150124 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:17:10.22412 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:17:10.324969 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:17:27.057343 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
starting worker pid=4014920 on localhost:11521 at 17:17:28.092
starting worker pid=4014919 on localhost:11521 at 17:17:28.297
2025-12-21 17:17:59.84917 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:18:18.806262 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:18:19.26263 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-21 17:18:19.271837 gannet.stats.ox.ac.uk 3986278 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=4019974 on localhost:11521 at 17:18:20.777
2025-12-21 17:18:37.610634 gannet.stats.ox.ac.uk 3986278 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 18.335 s.} ...
2025-12-21 17:18:37.621314 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=4021432 on localhost:11521 at 17:18:39.435
2025-12-21 17:18:54.511929 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 16.89 s.
2025-12-21 17:18:54.520722 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=4023001 on localhost:11521 at 17:18:55.353
2025-12-21 17:19:12.730582 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 18.21 s.
2025-12-21 17:19:12.738789 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 53.476 s.
2025-12-21 17:19:12.761729 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:19:12.804733 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-21 17:19:12.887784 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:19:12.920211 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-21 17:19:13.093878 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:19:13.334097 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-21 17:19:14.011354 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:19:23.545686 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:19:23.613 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-21 17:19:23.669314 gannet.stats.ox.ac.uk 3986278 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-21 r89216), detected cores: 24
2025-12-21 17:19:23.70406 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-21 17:19:23.838045 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-estimate_gps-15.R
2025-12-21 17:19:36.364128 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:19:51.67213 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=4028861 on localhost:11521 at 17:19:52.688
2025-12-21 17:20:09.452617 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 17.78 s.
2025-12-21 17:20:09.46382 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=4030898 on localhost:11521 at 17:20:10.040
2025-12-21 17:20:24.238665 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 14.775 s.
Saving _problems/test-estimate_mean_sd_nn-37.R
2025-12-21 17:20:24.413669 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:20:35.795772 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:20:50.365597 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=4035673 on localhost:11521 at 17:20:51.166
2025-12-21 17:21:05.243493 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 14.878 s.
2025-12-21 17:21:05.412154 gannet.stats.ox.ac.uk 3986278 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-21 17:21:22.098838 gannet.stats.ox.ac.uk 3986278 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=4039037 on localhost:11521 at 17:21:22.972
2025-12-21 17:21:42.425644 gannet.stats.ox.ac.uk 3986278 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 20.319 s.} ...
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-compute_deriv_nn.R:21:3'): compute_deriv_nn works as expected! ──
Expected `deriv_val[1, 1]` to equal 1.558466.
Differences:
`actual`: -1.0
`expected`: 1.6
── Failure ('test-compute_deriv_weights_gp.R:17:3'): compute_deriv_weights_gp works as expected! ──
Expected `weights[37]` to equal 3.307249e-05.
Differences:
`actual`: -0.00011
`expected`: 0.00003
── Failure ('test-compute_m_sigma.R:32:4'): compute_m_sigma works as expected! ──
Expected `gp_cerf[10]` to equal 2.105425.
Differences:
`actual`: -6.1
`expected`: 2.1
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Failure ('test-estimate_gps.R:15:3'): estimate_gps works as expected. ───────
Expected `gps_m$gps[4, 1]` to equal 8.74310154.
Differences:
`actual`: 7.3
`expected`: 8.7
── Failure ('test-estimate_mean_sd_nn.R:37:3'): estimate_mean_sd_nn works as expected! ──
Expected `val[10]` to equal 5.031225.
Differences:
`actual`: 5.067
`expected`: 5.031
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [139s/261s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-22 21:57:38.556257 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Saving _problems/test-compute_deriv_nn-21.R
2025-12-22 21:57:47.162173 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_deriv_weights_gp-17.R
2025-12-22 21:57:56.965034 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_m_sigma-32.R
2025-12-22 21:58:10.585884 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 21:58:18.570931 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 21:58:27.161705 gannet.stats.ox.ac.uk 514475 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=518790 on localhost:11101 at 21:58:27.559
2025-12-22 21:58:35.943547 gannet.stats.ox.ac.uk 514475 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 8.78100000000001 s.
2025-12-22 21:58:36.040664 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 21:58:44.035494 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 21:58:52.39717 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_weight_gp-49.R
2025-12-22 21:59:04.146656 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 21:59:13.174246 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 21:59:18.969826 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 21:59:23.577698 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 21:59:23.621475 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 21:59:31.93626 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 21:59:31.99279 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 21:59:32.043366 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 21:59:32.154228 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 21:59:32.217024 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 21:59:32.280203 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 21:59:32.334509 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 21:59:32.396317 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 21:59:39.136753 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
starting worker pid=523941 on localhost:11101 at 21:59:39.651
starting worker pid=523940 on localhost:11101 at 21:59:39.723
2025-12-22 21:59:56.866726 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 22:00:05.735506 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 22:00:05.758069 gannet.stats.ox.ac.uk 514475 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-22 22:00:05.814984 gannet.stats.ox.ac.uk 514475 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=525264 on localhost:11101 at 22:00:06.302
2025-12-22 22:00:13.655185 gannet.stats.ox.ac.uk 514475 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 7.833 s.} ...
2025-12-22 22:00:13.659385 gannet.stats.ox.ac.uk 514475 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=525635 on localhost:11101 at 22:00:14.131
2025-12-22 22:00:21.833248 gannet.stats.ox.ac.uk 514475 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 8.17400000000001 s.
2025-12-22 22:00:21.837238 gannet.stats.ox.ac.uk 514475 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=525968 on localhost:11101 at 22:00:22.355
2025-12-22 22:00:31.675673 gannet.stats.ox.ac.uk 514475 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 9.839 s.
2025-12-22 22:00:31.683465 gannet.stats.ox.ac.uk 514475 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 25.925 s.
2025-12-22 22:00:31.694416 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 22:00:31.717022 gannet.stats.ox.ac.uk 514475 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-22 22:00:31.76209 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 22:00:31.786788 gannet.stats.ox.ac.uk 514475 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-22 22:00:31.846491 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 22:00:31.867239 gannet.stats.ox.ac.uk 514475 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-22 22:00:31.911947 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 22:00:38.26709 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 22:00:38.291032 gannet.stats.ox.ac.uk 514475 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-22 22:00:38.335542 gannet.stats.ox.ac.uk 514475 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2025-12-22 r89219), detected cores: 24
2025-12-22 22:00:38.35893 gannet.stats.ox.ac.uk 514475 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-22 22:00:38.464274 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-estimate_gps-15.R
2025-12-22 22:00:46.056387 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 22:00:53.899512 gannet.stats.ox.ac.uk 514475 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=527663 on localhost:11101 at 22:00:54.510
2025-12-22 22:01:01.947515 gannet.stats.ox.ac.uk 514475 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 8.048 s.
2025-12-22 22:01:01.955532 gannet.stats.ox.ac.uk 514475 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=528016 on localhost:11101 at 22:01:02.456
2025-12-22 22:01:10.818244 gannet.stats.ox.ac.uk 514475 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 8.863 s.
Saving _problems/test-estimate_mean_sd_nn-37.R
2025-12-22 22:01:10.919308 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 22:01:16.247048 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 22:01:24.185433 gannet.stats.ox.ac.uk 514475 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=529793 on localhost:11101 at 22:01:24.684
2025-12-22 22:01:31.874528 gannet.stats.ox.ac.uk 514475 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 7.68899999999999 s.
2025-12-22 22:01:31.970045 gannet.stats.ox.ac.uk 514475 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-22 22:01:40.164582 gannet.stats.ox.ac.uk 514475 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=530687 on localhost:11101 at 22:01:40.671
2025-12-22 22:01:50.075663 gannet.stats.ox.ac.uk 514475 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 9.90700000000001 s.} ...
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-compute_deriv_nn.R:21:3'): compute_deriv_nn works as expected! ──
Expected `deriv_val[1, 1]` to equal 1.558466.
Differences:
`actual`: -1.0
`expected`: 1.6
── Failure ('test-compute_deriv_weights_gp.R:17:3'): compute_deriv_weights_gp works as expected! ──
Expected `weights[37]` to equal 3.307249e-05.
Differences:
`actual`: -0.00011
`expected`: 0.00003
── Failure ('test-compute_m_sigma.R:32:4'): compute_m_sigma works as expected! ──
Expected `gp_cerf[10]` to equal 2.105425.
Differences:
`actual`: -6.1
`expected`: 2.1
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Failure ('test-estimate_gps.R:15:3'): estimate_gps works as expected. ───────
Expected `gps_m$gps[4, 1]` to equal 8.74310154.
Differences:
`actual`: 7.3
`expected`: 8.7
── Failure ('test-estimate_mean_sd_nn.R:37:3'): estimate_mean_sd_nn works as expected! ──
Expected `val[10]` to equal 5.031225.
Differences:
`actual`: 5.067
`expected`: 5.031
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2.4
Check: tests
Result: ERROR
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-17 09:17:49.821386 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_nn-8.R
2025-12-17 09:17:51.096294 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_weights_gp-8.R
2025-12-17 09:17:51.929742 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_m_sigma-12.R
2025-12-17 09:17:52.750785 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_m_nn-10.R
2025-12-17 09:17:53.536041 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_sd_nn-10.R
2025-12-17 09:17:54.475887 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_gp-8.R
2025-12-17 09:17:55.223739 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_nn-8.R
2025-12-17 09:17:56.004034 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_sd_gp-17.R
Saving _problems/test-compute_weight_gp-49.R
2025-12-17 09:17:57.230403 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_gp-10.R
2025-12-17 09:17:58.024499 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_nngp-10.R
2025-12-17 09:17:58.827859 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_gps-10.R
2025-12-17 09:17:59.625059 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_mean_sd_nn-10.R
2025-12-17 09:18:00.363278 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_gp-11.R
2025-12-17 09:18:01.151327 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_nn-10.R
2025-12-17 09:18:01.983663 CRANWIN3 21552 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-find_optimal_nn-9.R
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compute_deriv_nn.R:5:3'): compute_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_deriv_weights_gp.R:5:3'): compute_deriv_weights_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_weights_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_m_sigma.R:9:4'): compute_m_sigma works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_m_sigma.R:9:4
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_m_nn.R:7:3'): compute_posterior_m_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_m_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_sd_nn.R:7:3'): compute_posterior_sd_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_gp.R:5:3'): compute_rl_deriv_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_nn.R:5:3'): compute_rl_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_sd_gp.R:14:4'): compute_sd_gp works as expected. ───────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_sd_gp.R:14:4
2. └─SuperLearner::SuperLearner(...)
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Error ('test-estimate_cerf_gp.R:7:3'): estimate_cerf_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_gp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_cerf_nngp.R:7:3'): estimate_cerf_nngp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_nngp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_gps.R:7:3'): estimate_gps works as expected. ──────────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_gps.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_mean_sd_nn.R:7:3'): estimate_mean_sd_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_mean_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_gp.R:8:3'): estimate_noise_gp works as expected ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_gp.R:8:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_nn.R:7:3'): estimate_noise_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-find_optimal_nn.R:6:3'): find_optimal_nn works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-find_optimal_nn.R:6:3
2. └─SuperLearner::SuperLearner(...)
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.2.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'A-Note-on-Choosing-Hyperparameters.Rmd' using rmarkdown
--- finished re-building 'A-Note-on-Choosing-Hyperparameters.Rmd'
--- re-building 'Developers-Guide.Rmd' using rmarkdown
--- finished re-building 'Developers-Guide.Rmd'
--- re-building 'GPCERF.Rmd' using rmarkdown
2025-12-17 09:18:12.002599 CRANWIN3 22520 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from GPCERF.Rmd:38-45 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GPCERF.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building 'GPCERF.Rmd'
--- re-building 'Nearest-neighbor-Gaussian-Processes.Rmd' using rmarkdown
2025-12-17 09:18:18.88815 CRANWIN3 17560 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Nearest-neighbor-Gaussian-Processes.Rmd:83-92 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Nearest-neighbor-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building 'Nearest-neighbor-Gaussian-Processes.Rmd'
--- re-building 'Standard-Gaussian-Processes.Rmd' using rmarkdown
2025-12-17 09:18:25.230098 CRANWIN3 17596 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Standard-Gaussian-Processes.Rmd:83-93 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Standard-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building 'Standard-Gaussian-Processes.Rmd'
SUMMARY: processing the following files failed:
'GPCERF.Rmd' 'Nearest-neighbor-Gaussian-Processes.Rmd'
'Standard-Gaussian-Processes.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [85s/154s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-24 05:56:02.233677 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Saving _problems/test-compute_deriv_nn-21.R
2025-12-24 05:56:09.007578 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_deriv_weights_gp-17.R
2025-12-24 05:56:14.153259 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_m_sigma-32.R
2025-12-24 05:56:22.844967 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 05:56:27.920341 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 05:56:32.622691 gimli2 1420650 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=1431728 on localhost:11719 at 05:56:32.991
2025-12-24 05:56:36.649458 gimli2 1420650 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 4.027 s.
2025-12-24 05:56:36.737625 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 05:56:41.547067 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 05:56:46.629246 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_weight_gp-49.R
2025-12-24 05:56:51.321513 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 05:56:56.117462 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:56:59.477813 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 05:57:02.702593 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:57:02.738006 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 05:57:07.60434 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:57:07.632369 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:57:07.668262 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:57:07.710548 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:57:07.746562 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:57:07.768637 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:57:07.805045 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:57:07.833274 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 05:57:12.652657 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
starting worker pid=1442145 on localhost:11719 at 05:57:13.073
starting worker pid=1442146 on localhost:11719 at 05:57:13.094
2025-12-24 05:57:20.96564 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 05:57:26.27615 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:57:26.283433 gimli2 1420650 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-24 05:57:26.287799 gimli2 1420650 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=1445237 on localhost:11719 at 05:57:26.636
2025-12-24 05:57:31.265884 gimli2 1420650 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 4.976 s.} ...
2025-12-24 05:57:31.268247 gimli2 1420650 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=1447064 on localhost:11719 at 05:57:31.653
2025-12-24 05:57:35.08694 gimli2 1420650 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.818 s.
2025-12-24 05:57:35.089378 gimli2 1420650 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=1448188 on localhost:11719 at 05:57:35.553
2025-12-24 05:57:40.709281 gimli2 1420650 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 5.61999999999999 s.
2025-12-24 05:57:40.717003 gimli2 1420650 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 14.428 s.
2025-12-24 05:57:40.726354 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:57:40.737785 gimli2 1420650 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-24 05:57:40.777482 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:57:40.791359 gimli2 1420650 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-24 05:57:40.862303 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:57:40.873276 gimli2 1420650 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-24 05:57:40.902886 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 05:57:44.789201 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:57:44.801359 gimli2 1420650 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-24 05:57:44.827223 gimli2 1420650 GPCERF log_system_info INFO: System name: Linux, OS type: unix, machine architecture: x86_64, user: hornik, R version 4.5.2 Patched (2025-12-21 r89220), detected cores: 32
2025-12-24 05:57:44.839198 gimli2 1420650 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-24 05:57:44.902013 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-estimate_gps-15.R
2025-12-24 05:57:50.86983 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 05:57:55.766333 gimli2 1420650 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=1452950 on localhost:11719 at 05:57:56.305
2025-12-24 05:58:00.225276 gimli2 1420650 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 4.459 s.
2025-12-24 05:58:00.227682 gimli2 1420650 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=1454140 on localhost:11719 at 05:58:00.569
2025-12-24 05:58:05.400198 gimli2 1420650 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 5.173 s.
Saving _problems/test-estimate_mean_sd_nn-37.R
2025-12-24 05:58:05.539531 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 05:58:09.266581 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 05:58:13.639235 gimli2 1420650 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=1457585 on localhost:11719 at 05:58:14.165
2025-12-24 05:58:17.747804 gimli2 1420650 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 4.108 s.
2025-12-24 05:58:17.796478 gimli2 1420650 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 05:58:23.435733 gimli2 1420650 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=1461182 on localhost:11719 at 05:58:23.837
2025-12-24 05:58:29.551028 gimli2 1420650 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 6.11199999999999 s.} ...
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-compute_deriv_nn.R:21:3'): compute_deriv_nn works as expected! ──
Expected `deriv_val[1, 1]` to equal 1.558466.
Differences:
`actual`: -1.0
`expected`: 1.6
── Failure ('test-compute_deriv_weights_gp.R:17:3'): compute_deriv_weights_gp works as expected! ──
Expected `weights[37]` to equal 3.307249e-05.
Differences:
`actual`: -0.00011
`expected`: 0.00003
── Failure ('test-compute_m_sigma.R:32:4'): compute_m_sigma works as expected! ──
Expected `gp_cerf[10]` to equal 2.105425.
Differences:
`actual`: -6.1
`expected`: 2.1
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Failure ('test-estimate_gps.R:15:3'): estimate_gps works as expected. ───────
Expected `gps_m$gps[4, 1]` to equal 8.74310154.
Differences:
`actual`: 7.3
`expected`: 8.7
── Failure ('test-estimate_mean_sd_nn.R:37:3'): estimate_mean_sd_nn works as expected! ──
Expected `val[10]` to equal 5.031225.
Differences:
`actual`: 5.067
`expected`: 5.031
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
Error:
! Test failures.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.2.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [27s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-13 05:44:57.923033 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_nn-8.R
2025-12-13 05:45:00.416523 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_deriv_weights_gp-8.R
2025-12-13 05:45:01.93277 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_m_sigma-12.R
2025-12-13 05:45:03.526912 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_m_nn-10.R
2025-12-13 05:45:05.100099 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_posterior_sd_nn-10.R
2025-12-13 05:45:06.917073 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_gp-8.R
2025-12-13 05:45:08.314523 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_rl_deriv_nn-8.R
2025-12-13 05:45:09.767577 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-compute_sd_gp-17.R
Saving _problems/test-compute_weight_gp-49.R
2025-12-13 05:45:13.986624 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_gp-10.R
2025-12-13 05:45:15.681828 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_cerf_nngp-10.R
2025-12-13 05:45:17.029967 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_gps-10.R
2025-12-13 05:45:18.675501 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_mean_sd_nn-10.R
2025-12-13 05:45:20.369581 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_gp-11.R
2025-12-13 05:45:22.178111 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-estimate_noise_nn-10.R
2025-12-13 05:45:24.016171 gimli2 260556 GPCERF estimate_gps INFO: Started estimating GPS values ...
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Error in xgboost::xgboost(data = xgmat, objective = objective, nrounds = ntrees, :
argument "y" is missing, with no default
Saving _problems/test-find_optimal_nn-9.R
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compute_deriv_nn.R:5:3'): compute_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_deriv_weights_gp.R:5:3'): compute_deriv_weights_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_deriv_weights_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_m_sigma.R:9:4'): compute_m_sigma works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_m_sigma.R:9:4
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_m_nn.R:7:3'): compute_posterior_m_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_m_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_posterior_sd_nn.R:7:3'): compute_posterior_sd_nn works as expected. ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_posterior_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_gp.R:5:3'): compute_rl_deriv_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_gp.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_rl_deriv_nn.R:5:3'): compute_rl_deriv_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_rl_deriv_nn.R:5:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-compute_sd_gp.R:14:4'): compute_sd_gp works as expected. ───────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-compute_sd_gp.R:14:4
2. └─SuperLearner::SuperLearner(...)
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Error ('test-estimate_cerf_gp.R:7:3'): estimate_cerf_gp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_gp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_cerf_nngp.R:7:3'): estimate_cerf_nngp works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_cerf_nngp.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_gps.R:7:3'): estimate_gps works as expected. ──────────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_gps.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_mean_sd_nn.R:7:3'): estimate_mean_sd_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_mean_sd_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_gp.R:8:3'): estimate_noise_gp works as expected ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_gp.R:8:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-estimate_noise_nn.R:7:3'): estimate_noise_nn works as expected! ──
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-estimate_noise_nn.R:7:3
2. └─SuperLearner::SuperLearner(...)
── Error ('test-find_optimal_nn.R:6:3'): find_optimal_nn works as expected! ────
Error in `SuperLearner::SuperLearner(Y = w_all, X = as.data.frame(cov_mt), SL.library = sl_lib)`: All algorithms dropped from library
Backtrace:
▆
1. └─GPCERF::estimate_gps(...) at test-find_optimal_nn.R:6:3
2. └─SuperLearner::SuperLearner(...)
[ FAIL 16 | WARN 752 | SKIP 0 | PASS 45 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.2.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘A-Note-on-Choosing-Hyperparameters.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘A-Note-on-Choosing-Hyperparameters.Rmd’
--- re-building ‘Developers-Guide.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Developers-Guide.Rmd’
--- re-building ‘GPCERF.Rmd’ using rmarkdown
2025-12-13 05:45:38.029637 gimli2 274017 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from GPCERF.Rmd:38-45 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GPCERF.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘GPCERF.Rmd’
--- re-building ‘Nearest-neighbor-Gaussian-Processes.Rmd’ using rmarkdown
2025-12-13 05:45:48.80051 gimli2 275346 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Nearest-neighbor-Gaussian-Processes.Rmd:83-92 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Nearest-neighbor-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘Nearest-neighbor-Gaussian-Processes.Rmd’
--- re-building ‘Standard-Gaussian-Processes.Rmd’ using rmarkdown
2025-12-13 05:45:58.960181 gimli2 277514 GPCERF estimate_gps INFO: Started estimating GPS values ...
Quitting from Standard-Gaussian-Processes.Rmd:83-93 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `SuperLearner::SuperLearner()`:
! All algorithms dropped from library
---
Backtrace:
▆
1. └─GPCERF::estimate_gps(...)
2. └─SuperLearner::SuperLearner(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Standard-Gaussian-Processes.Rmd' failed with diagnostics:
All algorithms dropped from library
--- failed re-building ‘Standard-Gaussian-Processes.Rmd’
SUMMARY: processing the following files failed:
‘GPCERF.Rmd’ ‘Nearest-neighbor-Gaussian-Processes.Rmd’
‘Standard-Gaussian-Processes.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.2.4
Check: tests
Result: ERROR
Running 'testthat.R' [136s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-23 07:43:14.359744 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Saving _problems/test-compute_deriv_nn-21.R
2025-12-23 07:43:20.103459 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_deriv_weights_gp-17.R
2025-12-23 07:43:25.167228 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_m_sigma-32.R
2025-12-23 07:43:33.503365 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-23 07:43:38.879309 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-23 07:43:44.062544 CRANWIN3 94520 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=89532 on localhost:11158 at 07:43:44.306
2025-12-23 07:43:46.640411 CRANWIN3 94520 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.57 s.
2025-12-23 07:43:46.690621 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-23 07:43:51.601896 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-23 07:43:56.74521 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_weight_gp-49.R
2025-12-23 07:44:01.774733 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-23 07:44:06.697567 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:10.226652 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-23 07:44:14.082476 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:14.09877 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-23 07:44:19.553501 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:19.564809 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:19.575163 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:19.584404 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:19.595093 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:19.605888 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:19.615636 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:19.626997 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-23 07:44:24.801058 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
starting worker pid=55836 on localhost:11158 at 07:44:25.001
starting worker pid=26208 on localhost:11158 at 07:44:25.030
2025-12-23 07:44:31.423736 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-23 07:44:36.630664 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:36.633874 CRANWIN3 94520 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-23 07:44:36.638732 CRANWIN3 94520 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=34812 on localhost:11158 at 07:44:36.880
2025-12-23 07:44:39.324754 CRANWIN3 94520 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 2.67999999999999 s.} ...
2025-12-23 07:44:39.327282 CRANWIN3 94520 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=38704 on localhost:11158 at 07:44:39.557
2025-12-23 07:44:41.915087 CRANWIN3 94520 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.58 s.
2025-12-23 07:44:41.917936 CRANWIN3 94520 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=16412 on localhost:11158 at 07:44:42.193
2025-12-23 07:44:45.410438 CRANWIN3 94520 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 3.5 s.
2025-12-23 07:44:45.413269 CRANWIN3 94520 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 8.78 s.
2025-12-23 07:44:45.418901 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:45.422757 CRANWIN3 94520 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-23 07:44:45.435693 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:45.437996 CRANWIN3 94520 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-23 07:44:45.471109 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:45.473312 CRANWIN3 94520 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-23 07:44:45.482181 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-23 07:44:49.73791 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:49.740339 CRANWIN3 94520 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-23 07:44:49.750846 CRANWIN3 94520 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.5.2 (2025-10-31 ucrt), detected cores: 96
2025-12-23 07:44:49.753169 CRANWIN3 94520 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-23 07:44:49.784656 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-estimate_gps-15.R
2025-12-23 07:44:54.970807 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-23 07:45:00.521952 CRANWIN3 94520 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=57676 on localhost:11158 at 07:45:00.757
2025-12-23 07:45:03.29064 CRANWIN3 94520 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.75999999999999 s.
2025-12-23 07:45:03.292875 CRANWIN3 94520 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=79836 on localhost:11158 at 07:45:03.493
2025-12-23 07:45:06.354683 CRANWIN3 94520 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 3.07000000000001 s.
Saving _problems/test-estimate_mean_sd_nn-37.R
2025-12-23 07:45:06.415181 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-23 07:45:10.479142 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-23 07:45:15.274752 CRANWIN3 94520 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=23252 on localhost:11158 at 07:45:15.548
2025-12-23 07:45:18.187099 CRANWIN3 94520 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 2.89999999999999 s.
2025-12-23 07:45:18.218886 CRANWIN3 94520 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-23 07:45:23.572227 CRANWIN3 94520 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=96612 on localhost:11158 at 07:45:23.850
2025-12-23 07:45:26.988348 CRANWIN3 94520 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 3.41999999999999 s.} ...
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-compute_deriv_nn.R:21:3'): compute_deriv_nn works as expected! ──
Expected `deriv_val[1, 1]` to equal 1.558466.
Differences:
`actual`: -1.0
`expected`: 1.6
── Failure ('test-compute_deriv_weights_gp.R:17:3'): compute_deriv_weights_gp works as expected! ──
Expected `weights[37]` to equal 3.307249e-05.
Differences:
`actual`: -0.00011
`expected`: 0.00003
── Failure ('test-compute_m_sigma.R:32:4'): compute_m_sigma works as expected! ──
Expected `gp_cerf[10]` to equal 2.105425.
Differences:
`actual`: -6.1
`expected`: 2.1
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Failure ('test-estimate_gps.R:15:3'): estimate_gps works as expected. ───────
Expected `gps_m$gps[4, 1]` to equal 8.74310154.
Differences:
`actual`: 7.3
`expected`: 8.7
── Failure ('test-estimate_mean_sd_nn.R:37:3'): estimate_mean_sd_nn works as expected! ──
Expected `val[10]` to equal 5.031225.
Differences:
`actual`: 5.067
`expected`: 5.031
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.2.4
Check: tests
Result: ERROR
Running 'testthat.R' [209s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(GPCERF)
>
> test_check("GPCERF")
2025-12-24 12:06:17.070682 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
Loading required package: nnls
Saving _problems/test-compute_deriv_nn-21.R
2025-12-24 12:06:25.362538 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_deriv_weights_gp-17.R
2025-12-24 12:06:34.214186 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_m_sigma-32.R
2025-12-24 12:06:46.55157 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 12:06:54.717796 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 12:07:03.106524 CRANWIN2 18568 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=77584 on localhost:11821 at 12:07:03.429
2025-12-24 12:07:06.868679 CRANWIN2 18568 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.76 s.
2025-12-24 12:07:06.923477 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 12:07:14.941586 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 12:07:23.619206 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-compute_weight_gp-49.R
2025-12-24 12:07:31.908482 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 12:07:39.457051 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:07:44.745028 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 12:07:51.583295 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:07:51.607923 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 12:07:59.630206 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:07:59.647258 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:07:59.665016 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:07:59.682822 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:07:59.700961 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:07:59.719322 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:07:59.737843 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:07:59.759488 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 12:08:07.845885 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
starting worker pid=74904 on localhost:11821 at 12:08:08.184
starting worker pid=37976 on localhost:11821 at 12:08:08.205
2025-12-24 12:08:17.116369 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 12:08:25.390601 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:08:25.39417 CRANWIN2 18568 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-24 12:08:25.471506 CRANWIN2 18568 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=94484 on localhost:11821 at 12:08:25.852
2025-12-24 12:08:29.743076 CRANWIN2 18568 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 4.27000000000001 s.} ...
2025-12-24 12:08:29.746608 CRANWIN2 18568 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=46964 on localhost:11821 at 12:08:30.019
2025-12-24 12:08:33.247613 CRANWIN2 18568 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.5 s.
2025-12-24 12:08:33.251011 CRANWIN2 18568 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=29156 on localhost:11821 at 12:08:33.609
2025-12-24 12:08:38.290541 CRANWIN2 18568 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 5.05000000000001 s.
2025-12-24 12:08:38.292491 CRANWIN2 18568 GPCERF estimate_cerf_nngp INFO: Done with estimating cerf using nngp approach Wall clock time: 12.91 s.
2025-12-24 12:08:38.295923 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:08:38.298036 CRANWIN2 18568 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-24 12:08:38.308549 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:08:38.310745 CRANWIN2 18568 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-24 12:08:38.352045 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:08:38.355327 CRANWIN2 18568 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-24 12:08:38.372038 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 12:08:45.158441 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:08:45.16208 CRANWIN2 18568 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-24 12:08:45.180947 CRANWIN2 18568 GPCERF log_system_info INFO: System name: Windows, OS type: windows, machine architecture: x86-64, user: CRAN, R version 4.4.3 (2025-02-28 ucrt), detected cores: 56
2025-12-24 12:08:45.184941 CRANWIN2 18568 GPCERF estimate_cerf_nngp INFO: Working on estimating cerf using nngp approach ...
2025-12-24 12:08:45.226221 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
Saving _problems/test-estimate_gps-15.R
2025-12-24 12:08:53.359796 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 12:09:01.497112 CRANWIN2 18568 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=41520 on localhost:11821 at 12:09:01.784
2025-12-24 12:09:05.249726 CRANWIN2 18568 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.75 s.
2025-12-24 12:09:05.253028 CRANWIN2 18568 GPCERF estimate_mean_sd_nn INFO: Working on estimating mean and sd using nngp approach ...
starting worker pid=96540 on localhost:11821 at 12:09:05.529
2025-12-24 12:09:09.192135 CRANWIN2 18568 GPCERF estimate_mean_sd_nn INFO: Done with estimating mean and sd using nngp approach Wall clock time: 3.94999999999999 s.
Saving _problems/test-estimate_mean_sd_nn-37.R
2025-12-24 12:09:09.260614 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 12:09:16.007441 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 12:09:24.201847 CRANWIN2 18568 GPCERF estimate_noise_nn INFO: Working on estimating residual error with nngp ...
starting worker pid=95384 on localhost:11821 at 12:09:24.524
2025-12-24 12:09:28.180538 CRANWIN2 18568 GPCERF estimate_noise_nn INFO: Done with estimating residual error with nngpWall clock time: 3.99000000000001 s.
2025-12-24 12:09:28.211805 CRANWIN2 18568 GPCERF estimate_gps INFO: Started estimating GPS values ...
2025-12-24 12:09:36.632002 CRANWIN2 18568 GPCERF find_optimal_nn INFO: Started finding optimal values ...
starting worker pid=60404 on localhost:11821 at 12:09:36.915
2025-12-24 12:09:41.357486 CRANWIN2 18568 GPCERF find_optimal_nn INFO: Done with finding optimal value.(Wall clock time: 4.72 s.} ...
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-compute_deriv_nn.R:21:3'): compute_deriv_nn works as expected! ──
Expected `deriv_val[1, 1]` to equal 1.558466.
Differences:
`actual`: -1.0
`expected`: 1.6
── Failure ('test-compute_deriv_weights_gp.R:17:3'): compute_deriv_weights_gp works as expected! ──
Expected `weights[37]` to equal 3.307249e-05.
Differences:
`actual`: -0.00011
`expected`: 0.00003
── Failure ('test-compute_m_sigma.R:32:4'): compute_m_sigma works as expected! ──
Expected `gp_cerf[10]` to equal 2.105425.
Differences:
`actual`: -6.1
`expected`: 2.1
── Failure ('test-compute_weight_gp.R:49:3'): multiplication works ─────────────
Expected `weight$weight[28]` to equal 0.0002182767.
Differences:
`actual`: 0.00000
`expected`: 0.00022
── Failure ('test-estimate_gps.R:15:3'): estimate_gps works as expected. ───────
Expected `gps_m$gps[4, 1]` to equal 8.74310154.
Differences:
`actual`: 7.3
`expected`: 8.7
── Failure ('test-estimate_mean_sd_nn.R:37:3'): estimate_mean_sd_nn works as expected! ──
Expected `val[10]` to equal 5.031225.
Differences:
`actual`: 5.067
`expected`: 5.031
[ FAIL 6 | WARN 2 | SKIP 0 | PASS 101 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64