Running ‘testthat.R’ [85s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > 
  > library(testthat)
  > library(tinyVAST)
  > 
  > # Run tests
  > testthat::test_check("tinyVAST")
  Starting 2 test processes.
  > test-SAR.R: 
  > test-SAR.R: Attaching package: 'igraph'
  > test-SAR.R: 
  > test-SAR.R: The following objects are masked from 'package:stats':
  > test-SAR.R: 
  > test-SAR.R:     decompose, spectrum
  > test-SAR.R: 
  > test-SAR.R: The following object is masked from 'package:testthat':
  > test-SAR.R: 
  > test-SAR.R:     compare
  > test-SAR.R: 
  > test-SAR.R: The following object is masked from 'package:base':
  > test-SAR.R: 
  > test-SAR.R:     union
  > test-SAR.R: 
  > test-basic-fits.R: Read 0 records
  > test-basic-fits.R: NOTE: it is generally simpler to use specifyEquations() or cfa()
  > test-basic-fits.R:       see ?specifyEquations
  > test-basic-fits.R: Running optimizer_loop #1
  > test-basic-fits.R: Matching hessian patterns... Done
  > test-basic-fits.R: outer mgc:  139.7703 
  > test-basic-fits.R: outer mgc:  50.0049 
  > test-basic-fits.R: outer mgc:  10.49524 
  > test-basic-fits.R: outer mgc:  42.56898 
  > test-basic-fits.R: outer mgc:  33.02677 
  > test-basic-fits.R: outer mgc:  66.67452 
  > test-basic-fits.R: outer mgc:  14.43981 
  > test-basic-fits.R: outer mgc:  16.22027 
  > test-basic-fits.R: outer mgc:  6.067037 
  > test-basic-fits.R: outer mgc:  10.2619 
  > test-basic-fits.R: outer mgc:  6.263402 
  > test-basic-fits.R: outer mgc:  2.999899 
  > test-basic-fits.R: outer mgc:  8.677365 
  > test-basic-fits.R: outer mgc:  2.357661 
  > test-basic-fits.R: outer mgc:  0.1356342 
  > test-basic-fits.R: outer mgc:  0.03511879 
  > test-basic-fits.R: outer mgc:  0.01736614 
  > test-basic-fits.R: outer mgc:  0.0009654507 
  > test-basic-fits.R: outer mgc:  8.114833e-05 
  > test-basic-fits.R: Running newton_loop #1
  > test-basic-fits.R: outer mgc:  8.114833e-05 
  > test-basic-fits.R: outer mgc:  0.0358767 
  > test-basic-fits.R: outer mgc:  0.03591924 
  > test-basic-fits.R: outer mgc:  0.2250638 
  > test-basic-fits.R: outer mgc: 
  > test-basic-fits.R:  0.2253101 
  > test-basic-fits.R: outer mgc:  0.001985216 
  > test-basic-fits.R: outer mgc:  0.001994549 
  > test-basic-fits.R: outer mgc:  0.6193572 
  > test-basic-fits.R: outer mgc:  0.6193144 
  > test-basic-fits.R: outer mgc:  0.1342154 
  > test-basic-fits.R: outer mgc:  0.1341932 
  > test-basic-fits.R: Running sdreport
  > test-basic-fits.R: outer mgc:  0.03589794 
  > test-basic-fits.R: outer mgc:  0.03589794 
  > test-basic-fits.R: outer mgc:  0.2249827 
  > test-basic-fits.R: outer mgc:  0.2253912 
  > test-basic-fits.R: outer mgc:  0.001990268 
  > test-basic-fits.R: outer mgc:  0.001989501 
  > test-basic-fits.R: outer mgc:  0.6192763 
  > test-basic-fits.R: outer mgc:  0.6193958 
  > test-basic-fits.R: outer mgc:  0.1341343 
  > test-basic-fits.R: outer mgc:  0.1342744 
  > test-basic-fits.R: outer mgc:  1.688327e-11 
  > test-basic-fits.R: Read 0 records
  > test-basic-fits.R: NOTE: it is generally simpler to use specifyEquations() or cfa()
  > test-basic-fits.R:       see ?specifyEquations
  > test-basic-fits.R: Running optimizer_loop #1
  > test-basic-fits.R: Matching hessian patterns... 
  > test-basic-fits.R: Done
  > test-basic-fits.R: outer mgc:  56569.33 
  > test-basic-fits.R: outer mgc:  1273 
  > test-basic-fits.R: outer mgc:  24820.02 
  > test-basic-fits.R: outer mgc:  26004.83 
  > test-basic-fits.R: outer mgc:  19430.3 
  > test-basic-fits.R: outer mgc: 
  > test-basic-fits.R:  5033.068 
  > test-basic-fits.R: outer mgc:  2810.923 
  > test-basic-fits.R: outer mgc:  474.8056 
  > test-basic-fits.R: outer mgc:  6253.602 
  > test-basic-fits.R: outer mgc:  6107.439 
  > test-basic-fits.R: outer mgc:  61.63476 
  > test-basic-fits.R: outer mgc:  2488.894 
  > test-basic-fits.R: outer mgc:  626.5097 
  > test-basic-fits.R: outer mgc:  1218.44 
  > test-basic-fits.R: outer mgc:  657.8356 
  > test-basic-fits.R: outer mgc:  702.0894 
  > test-basic-fits.R: outer mgc:  2786.819 
  > test-basic-fits.R: outer mgc:  682.1724 
  > test-basic-fits.R: outer mgc:  3052.84 
  > test-basic-fits.R: outer mgc:  1430.854 
  > test-basic-fits.R: outer mgc:  173.5428 
  > test-basic-fits.R: outer mgc: 
  > test-basic-fits.R:  243.2674 
  > test-basic-fits.R: outer mgc:  30.15947 
  > test-basic-fits.R: outer mgc:  12.99486 
  > test-basic-fits.R: outer mgc:  3.260848 
  > test-basic-fits.R: outer mgc:  0.2557589 
  > test-basic-fits.R: outer mgc:  0.0224636 
  > test-basic-fits.R: outer mgc:  0.0003993406 
  > test-basic-fits.R: outer mgc:  0.0003993406 
  > test-basic-fits.R: Running newton_loop #1
  > test-basic-fits.R: outer mgc:  10.41578 
  > test-basic-fits.R: outer mgc:  10.41499 
  > test-basic-fits.R: outer mgc:  420.1269 
  > test-basic-fits.R: outer mgc:  420.1261 
  > test-basic-fits.R: outer mgc:  4715.552 
  > test-basic-fits.R: outer mgc:  4715.551 
  > test-basic-fits.R: outer mgc:  47003.78 
  > test-basic-fits.R: outer mgc:  47003.78 
  > test-basic-fits.R: outer mgc:  0.4409364 
  > test-basic-fits.R: outer mgc:  0.4432772 
  > test-basic-fits.R: outer mgc:  0.6367845 
  > test-basic-fits.R: outer mgc:  0.6369055 
  > test-basic-fits.R: outer mgc:  0.4539012 
  > test-basic-fits.R: outer mgc: 
  > test-basic-fits.R:  0.4511987 
  > test-basic-fits.R: Running sdreport
  > test-basic-fits.R: outer mgc:  10.41538 
  > test-basic-fits.R: outer mgc:  10.41538 
  > test-basic-fits.R: outer mgc:  420.1265 
  > test-basic-fits.R: outer mgc:  420.1265 
  > test-basic-fits.R: outer mgc:  4715.551 
  > test-basic-fits.R: outer mgc:  4715.551 
  > test-basic-fits.R: outer mgc:  47003.78 
  > test-basic-fits.R: outer mgc:  47003.78 
  > test-basic-fits.R: outer mgc:  0.4413403 
  > test-basic-fits.R: outer mgc:  0.4428824 
  > test-basic-fits.R: outer mgc:  0.6367665 
  > test-basic-fits.R: outer mgc:  0.6369234 
  > test-basic-fits.R: outer mgc:  0.4535091 
  > test-basic-fits.R: outer mgc:  0.4516052 
  > test-basic-fits.R: outer mgc:  1.369145e-09 
  > test-basic-fits.R: Read 0 records
  > test-basic-fits.R: NOTE: it is generally simpler to use specifyEquations() or cfa()
  > test-basic-fits.R:       see ?specifyEquations
  > test-basic-fits.R: Running optimizer_loop #1
  > test-basic-fits.R: Matching hessian patterns... 
  > test-basic-fits.R: Done
  > test-basic-fits.R: outer mgc:  56569.33 
  > test-basic-fits.R: outer mgc:  1273 
  > test-deviance-residuals.R: Student-t degrees of freedom parameter will be estimated. This used to be fixed at 3 by default. To fix it, supply a value to `df` (e.g., `df = 3`).
  > test-basic-fits.R: outer mgc:  24820.02 
  > test-basic-fits.R: outer mgc:  26004.83 
  > test-basic-fits.R: outer mgc:  19430.3 
  > test-basic-fits.R: outer mgc:  5033.068 
  > test-basic-fits.R: outer mgc:  2810.923 
  > test-basic-fits.R: outer mgc:  474.8056 
  > test-deviance-residuals.R: Student-t degrees of freedom parameter fixed at 7.81030735915445. To estimate it, set `df = NULL`.
  > test-basic-fits.R: outer mgc:  6253.602 
  > test-basic-fits.R: outer mgc:  6107.439 
  > test-basic-fits.R: outer mgc:  61.63476 
  > test-basic-fits.R: outer mgc:  2488.894 
  > test-deviance-residuals.R: Student-t degrees of freedom parameter fixed at 7.81030735915445. To estimate it, set `df = NULL`.
  > test-basic-fits.R: outer mgc:  626.5097 
  > test-basic-fits.R: outer mgc:  1218.44 
  > test-basic-fits.R: outer mgc:  657.8356 
  > test-basic-fits.R: outer mgc:  702.0894 
  > test-basic-fits.R: outer mgc:  2786.819 
  > test-basic-fits.R: outer mgc:  682.1724 
  > test-basic-fits.R: outer mgc:  3052.84 
  > test-basic-fits.R: outer mgc:  1430.854 
  > test-basic-fits.R: outer mgc: 
  > test-basic-fits.R:  173.5428 
  > test-basic-fits.R: outer mgc:  243.2674 
  > test-basic-fits.R: outer mgc:  30.15947 
  > test-basic-fits.R: outer mgc:  12.99486 
  > test-basic-fits.R: outer mgc:  3.260848 
  > test-basic-fits.R: outer mgc:  0.2557589 
  > test-basic-fits.R: outer mgc:  0.0224636 
  > test-basic-fits.R: outer mgc:  0.0003993406 
  > test-basic-fits.R: Running newton_loop #1
  > test-basic-fits.R: outer mgc:  0.0003993406 
  > test-basic-fits.R: outer mgc:  10.41578 
  > test-basic-fits.R: outer mgc:  10.41499 
  > test-basic-fits.R: outer mgc:  420.1269 
  > test-basic-fits.R: outer mgc:  420.1261 
  > test-basic-fits.R: outer mgc:  4715.552 
  > test-basic-fits.R: outer mgc:  4715.551 
  > test-basic-fits.R: outer mgc:  47003.78 
  > test-basic-fits.R: outer mgc:  47003.78 
  > test-basic-fits.R: outer mgc:  0.4409364 
  > test-basic-fits.R: outer mgc:  0.4432772 
  > test-basic-fits.R: outer mgc:  0.6367845 
  > test-basic-fits.R: outer mgc:  0.6369055 
  > test-basic-fits.R: outer mgc:  0.4539012 
  > test-basic-fits.R: outer mgc:  0.4511987 
  > test-basic-fits.R: Running sdreport
  > test-basic-fits.R: outer mgc:  10.41538 
  > test-basic-fits.R: outer mgc:  10.41538 
  > test-basic-fits.R: outer mgc:  420.1265 
  > test-basic-fits.R: outer mgc:  420.1265 
  > test-basic-fits.R: outer mgc:  4715.551 
  > test-basic-fits.R: outer mgc:  4715.551 
  > test-basic-fits.R: outer mgc:  47003.78 
  > test-basic-fits.R: outer mgc:  47003.78 
  > test-basic-fits.R: outer mgc:  0.4413403 
  > test-basic-fits.R: outer mgc:  0.4428824 
  > test-basic-fits.R: outer mgc:  0.6367665 
  > test-dsem.R: 
  > test-dsem.R: Attaching package: 'dsem'
  > test-dsem.R: 
  > test-dsem.R: The following objects are masked from 'package:tinyVAST':
  > test-dsem.R: 
  > test-dsem.R:     bering_sea, cAIC, lognormal, make_dsem_ram, tweedie
  > test-dsem.R: 
  > test-basic-fits.R: outer mgc:  0.6369234 
  > test-basic-fits.R: outer mgc:  0.4535091 
  > test-basic-fits.R: outer mgc:  0.4516052 
  > test-basic-fits.R: outer mgc:  1.369145e-09 
  > test-basic-fits.R: Read 0 records
  > test-basic-fits.R: NOTE: it is generally simpler to use specifyEquations() or cfa()
  > test-basic-fits.R:       see ?specifyEquations
  > test-basic-fits.R: Running optimizer_loop #1
  > test-basic-fits.R: Matching hessian patterns... 
  > test-basic-fits.R: Done
  > test-basic-fits.R: outer mgc:  329.5854 
  > test-basic-fits.R: outer mgc:  68.05303 
  > test-basic-fits.R: outer mgc: 
  > test-basic-fits.R:  18.1942 
  > test-basic-fits.R: outer mgc:  29.9166 
  > test-basic-fits.R: outer mgc:  43.11229 
  > test-basic-fits.R: outer mgc:  37.29186 
  > test-basic-fits.R: outer mgc:  39.28674 
  > test-basic-fits.R: outer mgc:  13.80786 
  > test-basic-fits.R: outer mgc:  56.23285 
  > test-basic-fits.R: outer mgc:  25.44009 
  > test-basic-fits.R: outer mgc:  7.885275 
  > test-basic-fits.R: outer mgc:  4.040772 
  > test-basic-fits.R: outer mgc:  3.719265 
  > test-basic-fits.R: outer mgc:  0.7612068 
  > test-basic-fits.R: outer mgc:  0.1442086 
  > test-basic-fits.R: outer mgc:  0.06999749 
  > test-basic-fits.R: outer mgc:  0.00454186 
  > test-basic-fits.R: outer mgc:  0.0009494951 
  > test-basic-fits.R: outer mgc: 
  > test-basic-fits.R:  0.0002300872 
  > test-basic-fits.R: outer mgc:  0.0002300872 
  > test-basic-fits.R: outer mgc:  0.03431448 
  > test-basic-fits.R: Running newton_loop #1
  > test-basic-fits.R: outer mgc:  0.03423211 
  > test-basic-fits.R: outer mgc:  0.0006446326 
  > test-basic-fits.R: outer mgc:  0.0006324035 
  > test-basic-fits.R: outer mgc:  0.0006472365 
  > test-basic-fits.R: outer mgc:  0.0006488188 
  > test-basic-fits.R: outer mgc:  0.0006098311 
  > test-basic-fits.R: outer mgc:  0.0006190326 
  > test-basic-fits.R: outer mgc:  0.2221437 
  > test-basic-fits.R: outer mgc:  0.2229958 
  > test-basic-fits.R: outer mgc:  0.636537 
  > test-basic-fits.R: outer mgc:  0.6371541 
  > test-basic-fits.R: outer mgc:  0.1350653 
  > test-basic-fits.R: outer mgc:  0.1356602 
  > test-basic-fits.R: Running sdreport
  > test-basic-fits.R: outer mgc:  0.03427353 
  > test-basic-fits.R: outer mgc:  0.03427353 
  > test-basic-fits.R: outer mgc:  0.0006385177 
  > test-basic-fits.R: outer mgc:  0.0006385177 
  Saving _problems/test-dsem-35.R
  Saving _problems/test-dsem-107.R
  > test-basic-fits.R: outer mgc:  0.0006480273 
  > test-basic-fits.R: outer mgc:  0.0006480273 
  > test-basic-fits.R: outer mgc:  0.0006144316 
  > test-basic-fits.R: outer mgc:  0.0006144316 
  > test-basic-fits.R: outer mgc:  0.222374 
  > test-basic-fits.R: outer mgc:  0.2227659 
  > test-basic-fits.R: outer mgc:  0.6367665 
  > test-basic-fits.R: outer mgc:  0.6369234 
  > test-basic-fits.R: outer mgc:  0.1352949 
  > test-basic-fits.R: outer mgc:  0.1354297 
  > test-basic-fits.R: outer mgc: 
  > test-basic-fits.R:  7.672857e-10 
  > test-basic-fits.R: Read 0 records
  > test-basic-fits.R: NOTE: it is generally simpler to use specifyEquations() or cfa()
  > test-basic-fits.R:       see ?specifyEquations
  > test-basic-fits.R: Running optimizer_loop #1
  > test-basic-fits.R: Matching hessian patterns... 
  > test-basic-fits.R: Done
  > test-basic-fits.R: outer mgc:  329.5854 
  > test-basic-fits.R: outer mgc:  68.05303 
  > test-basic-fits.R: outer mgc:  18.1942 
  > test-basic-fits.R: outer mgc:  29.9166 
  > test-basic-fits.R: outer mgc:  43.11229 
  > test-basic-fits.R: outer mgc:  37.29186 
  > test-basic-fits.R: outer mgc:  39.28674 
  > test-basic-fits.R: outer mgc:  13.80786 
  > test-basic-fits.R: outer mgc:  56.23285 
  > test-basic-fits.R: outer mgc: 
  > test-basic-fits.R:  25.44009 
  > test-basic-fits.R: outer mgc:  7.885275 
  > test-basic-fits.R: outer mgc:  4.040772 
  > test-basic-fits.R: outer mgc:  3.719265 
  > test-basic-fits.R: outer mgc:  0.7612068 
  > test-basic-fits.R: outer mgc:  0.1442086 
  > test-basic-fits.R: outer mgc:  0.06999749 
  > test-basic-fits.R: outer mgc:  0.00454186 
  > test-basic-fits.R: outer mgc:  0.0009494951 
  > test-basic-fits.R: outer mgc:  0.0002300872 
  > test-basic-fits.R: Running newton_loop #1
  > test-basic-fits.R: outer mgc:  0.0002300872 
  > test-basic-fits.R: outer mgc:  0.03431448 
  > test-basic-fits.R: outer mgc:  0.03423211 
  > test-basic-fits.R: outer mgc:  0.0006446326 
  > test-basic-fits.R: outer mgc:  0.0006324035 
  > test-basic-fits.R: outer mgc:  0.0006472365 
  > test-basic-fits.R: outer mgc:  0.0006488188 
  > test-basic-fits.R: outer mgc:  0.0006098311 
  > test-basic-fits.R: outer mgc: 
  > test-basic-fits.R:  0.0006190326 
  > test-basic-fits.R: outer mgc:  0.2221437 
  > test-basic-fits.R: outer mgc:  0.2229958 
  > test-basic-fits.R: outer mgc:  0.636537 
  > test-basic-fits.R: outer mgc:  0.6371541 
  > test-basic-fits.R: outer mgc:  0.1350653 
  > test-basic-fits.R: outer mgc: 
  > test-basic-fits.R:  0.1356602 
  > test-basic-fits.R: Running sdreport
  > test-basic-fits.R: outer mgc:  0.03427353 
  > test-basic-fits.R: outer mgc:  0.03427353 
  > test-basic-fits.R: outer mgc:  0.0006385177 
  > test-basic-fits.R: outer mgc:  0.0006385177 
  > test-basic-fits.R: outer mgc:  0.0006480273 
  > test-basic-fits.R: outer mgc:  0.0006480273 
  > test-basic-fits.R: outer mgc:  0.0006144316 
  > test-basic-fits.R: outer mgc:  0.0006144316 
  > test-basic-fits.R: outer mgc:  0.222374 
  > test-basic-fits.R: outer mgc:  0.2227659 
  > test-basic-fits.R: outer mgc:  0.6367665 
  > test-basic-fits.R: outer mgc:  0.6369234 
  > test-basic-fits.R: outer mgc:  0.1352949 
  > test-basic-fits.R: outer mgc:  0.1354297 
  > test-basic-fits.R: outer mgc:  7.672857e-10 
  > test-mesh.R: Linking to GEOS 3.14.1, GDAL 3.13.1, PROJ 9.8.1; sf_use_s2() is TRUE
  > test-index-standardization.R: Loading required package: VAST
  > test-platform.R: Call: 
  > test-platform.R: tinyVAST(formula = n ~ s(w), data = Data, space_term = "", spatial_domain = mesh, 
  > test-platform.R:     control = tinyVASTcontrol(getJointPrecision = TRUE))
  > test-platform.R: 
  > test-platform.R: Run time: 
  > test-platform.R: Time difference of 1.603303 secs
  > test-platform.R: 
  > test-platform.R: Family: 
  > test-platform.R: $obs
  > test-platform.R: 
  > test-platform.R: Family: gaussian 
  > test-platform.R: Link function: identity 
  > test-platform.R: 
  > test-platform.R: 
  > test-platform.R: 
  > test-platform.R: 
  > test-platform.R: sdreport(.) result
  > test-platform.R:                 Estimate Std. Error
  > test-platform.R: alpha_j     0.0009404264  0.1178307
  > test-platform.R: theta_z     1.0062973954  0.1055913
  > test-platform.R: log_lambda -2.4632150167  0.6906784
  > test-platform.R: log_sigma  -0.2433082708  0.1604643
  > test-platform.R: log_kappa   0.1683191083  0.2109439
  > test-platform.R: Maximum gradient component: 0.0004330321 
  > test-platform.R: 
  > test-platform.R: Proportion conditional deviance explained: 
  > test-platform.R: [1] 0.8706393
  > test-platform.R: 
  > test-platform.R: space_term: 
  > test-platform.R:   heads to from parameter start Estimate Std_Error  z_value      p_value
  > test-platform.R: 1     2  n    n         1  <NA> 1.006297 0.1055913 9.530119 1.571033e-21
  > test-platform.R: 
  > test-platform.R: Fixed terms: 
  > test-platform.R:                 Estimate Std_Error     z_value  p_value
  > test-platform.R: (Intercept) 0.0009404264 0.1178307 0.007981165 0.993632
  > test-platform.R: 
  > test-platform.R: Sanity check: 
  > test-platform.R: 
  > test-smooths.R: Gu & Wahba 4 term additive model
  > test-smooths.R: Gu & Wahba 4 term additive model
  > test-smooths.R: Gu & Wahba 4 term additive model
  [ FAIL 2 | WARN 3 | SKIP 20 | PASS 117 ]
  
  ══ Skipped tests (20) ══════════════════════════════════════════════════════════
  • On CRAN (19): 'test-deviance-residuals.R:3:3',
    'test-deviance-residuals.R:37:3', 'test-deviance-residuals.R:116:3',
    'test-deviance-residuals.R:151:3', 'test-deviance-residuals.R:189:3',
    'test-deviance-residuals.R:228:3', 'test-deviance-residuals.R:255:3',
    'test-deviance-residuals.R:313:3', 'test-deviance-residuals.R:352:3',
    'test-basic-fits.R:41:3', 'test-smooths.R:2:3', 'test-smooths.R:151:3',
    'test-smooths.R:167:3', 'test-smooths.R:177:3', 'test-smooths.R:194:3',
    'test-smooths.R:214:3', 'test-smooths.R:231:3', 'test-smooths.R:248:3',
    'test-smooths.R:268:3'
  • require(VAST) is not TRUE (1): 'test-index-standardization.R:77:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-dsem.R:30:3'): dsem and tinyVAST give identical results without lags ──
  Error in `dsem(tsdata = tsdat, family = c("normal", "normal"), sem = "X -> Y, 0, beta", control = dsem_control(run_model = FALSE, use_REML = FALSE))`: starting with release 3.0.0, `family` must be a named list of 
  Backtrace:
      ▆
   1. └─dsem::dsem(...) at test-dsem.R:30:3
  ── Error ('test-dsem.R:101:3'): dsem and tinyVAST give identical results with lags ──
  Error in `dsem(tsdata = tsdat, family = c("normal", "normal"), sem = "X -> Y, 1, beta", control = dsem_control(run_model = TRUE, use_REML = FALSE, nlminb_loops = 0, newton_loops = 0, getsd = FALSE, extra_convergence_checks = FALSE))`: starting with release 3.0.0, `family` must be a named list of 
  Backtrace:
      ▆
   1. └─dsem::dsem(...) at test-dsem.R:101:3
  
  [ FAIL 2 | WARN 3 | SKIP 20 | PASS 117 ]
  Error:
  ! Test failures.
  Execution halted