Running ‘testthat.R’ [240s/248s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CausalGPS)
  > 
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > test_check("CausalGPS")
  OMP: Warning #96: Cannot form a team with 8 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  2023-05-04 08:02:02.17335 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:02:13.208558 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 196) ... 
  2023-05-04 08:02:13.362125 gannet.stats.ox.ac.uk 2803706 CausalGPS FUN WARN:  There is no data to match with  19.9149974416582 in  0.5  radius.
  2023-05-04 08:02:13.658964 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 196)
  2023-05-04 08:02:18.199705 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:02:38.718684 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 490) ... 
  2023-05-04 08:02:38.729344 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 490)
  2023-05-04 08:02:38.772125 gannet.stats.ox.ac.uk 2803706 CausalGPS generate_pseudo_pop WARN:  Effective sample size is less than recommended.Current: 7.36082124077708, recommended min value: 49.
  2023-05-04 08:02:38.850479 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:02:41.731731 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 196) ... 
  2023-05-04 08:02:41.965843 gannet.stats.ox.ac.uk 2803706 CausalGPS FUN WARN:  There is no data to match with  21.2300763979248 in  0.5  radius.
  2023-05-04 08:02:42.211564 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 196)
  2023-05-04 08:02:43.3838 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 100) ... 
  2023-05-04 08:02:43.396586 gannet.stats.ox.ac.uk 2803706 CausalGPS FUN WARN:  There is no data to match with  -8.74760785492387 in  0.5  radius.
  2023-05-04 08:02:43.402276 gannet.stats.ox.ac.uk 2803706 CausalGPS FUN WARN:  There is no data to match with  -7.74760785492387 in  0.5  radius.
  2023-05-04 08:02:43.40793 gannet.stats.ox.ac.uk 2803706 CausalGPS FUN WARN:  There is no data to match with  -6.74760785492387 in  0.5  radius.
  2023-05-04 08:02:43.413652 gannet.stats.ox.ac.uk 2803706 CausalGPS FUN WARN:  There is no data to match with  -5.74760785492387 in  0.5  radius.
  2023-05-04 08:02:43.419181 gannet.stats.ox.ac.uk 2803706 CausalGPS FUN WARN:  There is no data to match with  -4.74760785492387 in  0.5  radius.
  2023-05-04 08:02:43.424792 gannet.stats.ox.ac.uk 2803706 CausalGPS FUN WARN:  There is no data to match with  -3.74760785492387 in  0.5  radius.
  2023-05-04 08:02:43.556018 gannet.stats.ox.ac.uk 2803706 CausalGPS FUN WARN:  There is no data to match with  21.2523921450761 in  0.5  radius.
  2023-05-04 08:02:43.561992 gannet.stats.ox.ac.uk 2803706 CausalGPS FUN WARN:  There is no data to match with  22.2523921450761 in  0.5  radius.
  2023-05-04 08:02:43.567816 gannet.stats.ox.ac.uk 2803706 CausalGPS FUN WARN:  There is no data to match with  23.2523921450761 in  0.5  radius.
  2023-05-04 08:02:43.823022 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 100)
  2023-05-04 08:02:43.836108 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 1000) ... 
  2023-05-04 08:02:43.84503 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 1000)
  2023-05-04 08:02:44.153469 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:03:00.17024 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 98) ... 
  2023-05-04 08:03:00.317812 gannet.stats.ox.ac.uk 2803706 CausalGPS FUN WARN:  There is no data to match with  17.0145640770203 in  0.5  radius.
  2023-05-04 08:03:00.58383 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 98)
  2023-05-04 08:03:00.789821 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:03:22.286761 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 98) ... 
  2023-05-04 08:03:22.457468 gannet.stats.ox.ac.uk 2803706 CausalGPS FUN WARN:  There is no data to match with  17.0145640770203 in  0.5  radius.
  2023-05-04 08:03:22.721605 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 98)
  2023-05-04 08:03:25.053335 gannet.stats.ox.ac.uk 2803706 CausalGPS estimate_gps WARN:  Vector w has 1 missing values.
  2023-05-04 08:03:25.124286 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:03:57.587362 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 392) ... 
  2023-05-04 08:03:58.176653 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 392)
  2023-05-04 08:04:03.766404 gannet.stats.ox.ac.uk 2803706 CausalGPS estimate_npmetric_erf INFO:  The band width with the minimum risk value: 2.
  2023-05-04 08:04:03.875073 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:04:36.447102 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 392) ... 
  2023-05-04 08:04:37.0496 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 392)
  2023-05-04 08:04:42.605619 gannet.stats.ox.ac.uk 2803706 CausalGPS estimate_npmetric_erf INFO:  The band width with the minimum risk value: 2.
  2023-05-04 08:04:42.939756 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:04:49.367976 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 490) ... 
  2023-05-04 08:04:49.961411 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 490)
  2023-05-04 08:04:50.009949 gannet.stats.ox.ac.uk 2803706 CausalGPS generate_pseudo_pop WARN:  Effective sample size is less than recommended.Current: 26.1426863179163, recommended min value: 49.
  2023-05-04 08:04:50.135055 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:04:53.264808 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 08:04:53.652356 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 08:04:53.727557 gannet.stats.ox.ac.uk 2803706 CausalGPS generate_pseudo_pop WARN:  Effective sample size is less than recommended.Current: 20.5023661048217, recommended min value: 46.
  2023-05-04 08:04:53.763427 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:04:53.798156 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:04:53.830215 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:04:53.860106 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:04:53.889814 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:04:53.928879 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:04:53.971754 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:04:54.004197 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:04:54.04536 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:04:57.207194 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 08:04:57.216995 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 08:04:57.265687 gannet.stats.ox.ac.uk 2803706 CausalGPS generate_pseudo_pop WARN:  Effective sample size is less than recommended.Current: 3.24100498567868, recommended min value: 46.
  2023-05-04 08:04:57.311871 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:05:00.402721 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 08:05:00.767968 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 08:05:03.911578 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 08:05:04.249674 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 08:05:07.25573 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 08:05:07.643827 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 08:05:11.195691 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 08:05:11.546588 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 08:05:11.593671 gannet.stats.ox.ac.uk 2803706 CausalGPS generate_pseudo_pop WARN:  Effective sample size is less than recommended.Current: 20.5161021345085, recommended min value: 46.
  2023-05-04 08:05:11.628022 gannet.stats.ox.ac.uk 2803706 CausalGPS log_system_info INFO:  System name: Linux, OS type: unix, machine architecture: x86_64, user: ripley, R Under development (unstable) (2023-05-04 r84388), detected cores: 24
  2023-05-04 08:05:13.384851 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 08:05:13.753865 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 08:05:15.566742 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 08:05:15.906902 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 08:05:17.735916 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 08:05:18.0808 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 08:05:19.852904 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 08:05:20.231203 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 08:05:21.99126 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 08:05:22.325391 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 08:05:24.102212 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 08:05:24.448823 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 08:05:26.20462 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 08:05:26.553703 gannet.stats.ox.ac.uk 2803706 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 08:05:26.575908 gannet.stats.ox.ac.uk 2803706 CausalGPS generate_pseudo_pop WARN:  Effective sample size is less than recommended.Current: 22.7748385392029, recommended min value: 46.
  [ FAIL 5 | WARN 88 | SKIP 0 | PASS 205 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-compile_pseudo_pop.R:65:3'): Compiling pseudo pop works as expected. ──
  mean(pseudo_pop_2$counter_weight) not equal to 0.7465975.
  1/1 mismatches
  [1] 0.746 - 0.747 == -0.000738
  ── Failure ('test-compute_density.R:10:3'): compute_density works ──────────────
  cd[10] not equal to 0.537411.
  1/1 mismatches
  [1] 0.537 - 0.537 == -0.000478
  ── Failure ('test-estimate_npmetric_erf.R:34:3'): estimate_npmetric_erf works as expected ──
  res$risk_val[1] not equal to 1305125.
  1/1 mismatches
  [1] 1304486 - 1305125 == -639
  ── Failure ('test-estimate_npmetric_erf.R:74:3'): estimate_npmetric_erf works as expected (with earth) ──
  res$risk_val[1] not equal to 1305125.
  1/1 mismatches
  [1] 1304486 - 1305125 == -639
  ── Failure ('test-generate_pseudo_pop.R:248:3'): generate_pseudo_pop works as expected. ──
  ps_pop3$adjusted_corr_results$mean_absolute_corr not equal to 0.3750209.
  1/1 mismatches
  [1] 0.375 - 0.375 == -1.21e-06
  
  [ FAIL 5 | WARN 88 | SKIP 0 | PASS 205 ]
  Error: Test failures
  Execution halted