Running ‘testthat.R’ [227s/242s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CausalGPS)
  > 
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > test_check("CausalGPS")
  2023-05-04 07:48:56.059382 gannet.stats.ox.ac.uk 2732123 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 07:49:06.390604 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 196) ... 
  2023-05-04 07:49:06.541175 gannet.stats.ox.ac.uk 2732123 CausalGPS FUN WARN:  There is no data to match with  19.9149974416582 in  0.5  radius.
  2023-05-04 07:49:06.833406 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 196)
  2023-05-04 07:49:10.936987 gannet.stats.ox.ac.uk 2732123 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 07:49:29.74087 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 490) ... 
  2023-05-04 07:49:29.752289 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 490)
  2023-05-04 07:49:29.797596 gannet.stats.ox.ac.uk 2732123 CausalGPS generate_pseudo_pop WARN:  Effective sample size is less than recommended.Current: 7.36082124077708, recommended min value: 49.
  2023-05-04 07:49:29.882178 gannet.stats.ox.ac.uk 2732123 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 07:49:32.880924 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 196) ... 
  2023-05-04 07:49:33.099911 gannet.stats.ox.ac.uk 2732123 CausalGPS FUN WARN:  There is no data to match with  21.2300763979248 in  0.5  radius.
  2023-05-04 07:49:33.42806 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 196)
  2023-05-04 07:49:34.916377 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 100) ... 
  2023-05-04 07:49:34.931438 gannet.stats.ox.ac.uk 2732123 CausalGPS FUN WARN:  There is no data to match with  -8.74760785492387 in  0.5  radius.
  2023-05-04 07:49:34.938222 gannet.stats.ox.ac.uk 2732123 CausalGPS FUN WARN:  There is no data to match with  -7.74760785492387 in  0.5  radius.
  2023-05-04 07:49:34.944683 gannet.stats.ox.ac.uk 2732123 CausalGPS FUN WARN:  There is no data to match with  -6.74760785492387 in  0.5  radius.
  2023-05-04 07:49:34.952188 gannet.stats.ox.ac.uk 2732123 CausalGPS FUN WARN:  There is no data to match with  -5.74760785492387 in  0.5  radius.
  2023-05-04 07:49:34.960294 gannet.stats.ox.ac.uk 2732123 CausalGPS FUN WARN:  There is no data to match with  -4.74760785492387 in  0.5  radius.
  2023-05-04 07:49:34.968268 gannet.stats.ox.ac.uk 2732123 CausalGPS FUN WARN:  There is no data to match with  -3.74760785492387 in  0.5  radius.
  2023-05-04 07:49:35.142653 gannet.stats.ox.ac.uk 2732123 CausalGPS FUN WARN:  There is no data to match with  21.2523921450761 in  0.5  radius.
  2023-05-04 07:49:35.151042 gannet.stats.ox.ac.uk 2732123 CausalGPS FUN WARN:  There is no data to match with  22.2523921450761 in  0.5  radius.
  2023-05-04 07:49:35.158948 gannet.stats.ox.ac.uk 2732123 CausalGPS FUN WARN:  There is no data to match with  23.2523921450761 in  0.5  radius.
  2023-05-04 07:49:35.452722 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 100)
  2023-05-04 07:49:35.466249 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 1000) ... 
  2023-05-04 07:49:35.476413 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 1000)
  2023-05-04 07:49:35.800935 gannet.stats.ox.ac.uk 2732123 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 07:49:51.60727 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 98) ... 
  2023-05-04 07:49:51.760457 gannet.stats.ox.ac.uk 2732123 CausalGPS FUN WARN:  There is no data to match with  17.0145640770203 in  0.5  radius.
  2023-05-04 07:49:52.034669 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 98)
  2023-05-04 07:49:52.213853 gannet.stats.ox.ac.uk 2732123 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 07:50:12.742698 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 98) ... 
  2023-05-04 07:50:12.915009 gannet.stats.ox.ac.uk 2732123 CausalGPS FUN WARN:  There is no data to match with  17.0145640770203 in  0.5  radius.
  2023-05-04 07:50:13.211862 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 98)
  2023-05-04 07:50:15.480068 gannet.stats.ox.ac.uk 2732123 CausalGPS estimate_gps WARN:  Vector w has 1 missing values.
  2023-05-04 07:50:15.54207 gannet.stats.ox.ac.uk 2732123 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 07:50:45.906271 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 392) ... 
  2023-05-04 07:50:46.53376 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 392)
  2023-05-04 07:50:52.115218 gannet.stats.ox.ac.uk 2732123 CausalGPS estimate_npmetric_erf INFO:  The band width with the minimum risk value: 2.
  2023-05-04 07:50:52.230489 gannet.stats.ox.ac.uk 2732123 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 07:51:23.665929 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 392) ... 
  2023-05-04 07:51:24.31898 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 392)
  2023-05-04 07:51:30.19133 gannet.stats.ox.ac.uk 2732123 CausalGPS estimate_npmetric_erf INFO:  The band width with the minimum risk value: 2.
  2023-05-04 07:51:30.462843 gannet.stats.ox.ac.uk 2732123 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 07:51:36.74642 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 490) ... 
  2023-05-04 07:51:37.443114 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 490)
  2023-05-04 07:51:37.528953 gannet.stats.ox.ac.uk 2732123 CausalGPS generate_pseudo_pop WARN:  Effective sample size is less than recommended.Current: 26.1426863179163, recommended min value: 49.
  2023-05-04 07:51:37.65063 gannet.stats.ox.ac.uk 2732123 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 07:51:40.754601 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 07:51:41.162418 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 07:51:41.214987 gannet.stats.ox.ac.uk 2732123 CausalGPS generate_pseudo_pop WARN:  Effective sample size is less than recommended.Current: 20.5023661048217, recommended min value: 46.
  2023-05-04 07:51:41.255593 gannet.stats.ox.ac.uk 2732123 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 07:51:41.288263 gannet.stats.ox.ac.uk 2732123 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 07:51:41.31967 gannet.stats.ox.ac.uk 2732123 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 07:51:41.349916 gannet.stats.ox.ac.uk 2732123 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 07:51:41.381691 gannet.stats.ox.ac.uk 2732123 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 07:51:41.411938 gannet.stats.ox.ac.uk 2732123 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 07:51:41.447341 gannet.stats.ox.ac.uk 2732123 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 07:51:41.513879 gannet.stats.ox.ac.uk 2732123 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 07:51:41.563865 gannet.stats.ox.ac.uk 2732123 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 07:51:44.672171 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 07:51:44.683077 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 07:51:44.732783 gannet.stats.ox.ac.uk 2732123 CausalGPS generate_pseudo_pop WARN:  Effective sample size is less than recommended.Current: 3.24100498567868, recommended min value: 46.
  2023-05-04 07:51:44.773479 gannet.stats.ox.ac.uk 2732123 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 07:51:47.814909 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 07:51:48.219494 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 07:51:51.198485 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 07:51:51.577245 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 07:51:54.927185 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 07:51:55.393772 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 07:51:58.593499 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 07:51:58.980291 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 07:51:59.026569 gannet.stats.ox.ac.uk 2732123 CausalGPS generate_pseudo_pop WARN:  Effective sample size is less than recommended.Current: 20.5161021345085, recommended min value: 46.
  2023-05-04 07:51:59.060673 gannet.stats.ox.ac.uk 2732123 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 07:52:00.95784 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 07:52:01.414178 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 07:52:03.281016 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 07:52:03.647749 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 07:52:05.545848 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 07:52:06.494423 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 07:52:08.314684 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 07:52:08.717326 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 07:52:10.468928 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 07:52:10.839811 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 07:52:12.694 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 07:52:13.11995 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 07:52:14.901719 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 460) ... 
  2023-05-04 07:52:15.285004 gannet.stats.ox.ac.uk 2732123 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 460)
  2023-05-04 07:52:15.307407 gannet.stats.ox.ac.uk 2732123 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