Last updated on 2026-07-01 12:52:34 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.6.0 | 262.59 | 569.32 | 831.91 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.6.0 | 198.05 | 456.96 | 655.01 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.6.1 | 179.00 | 625.52 | 804.52 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.6.1 | 308.00 | 589.31 | 897.31 | OK | |
| r-devel-windows-x86_64 | 1.6.1 | 232.00 | 521.00 | 753.00 | OK | |
| r-patched-linux-x86_64 | 1.6.0 | 248.05 | 594.01 | 842.06 | ERROR | |
| r-release-linux-x86_64 | 1.6.0 | ERROR | ||||
| r-release-macos-arm64 | 1.6.1 | 52.00 | 131.00 | 183.00 | OK | |
| r-release-macos-x86_64 | 1.6.1 | 10.00 | ERROR | |||
| r-release-windows-x86_64 | 1.6.0 | 244.00 | 617.00 | 861.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.6.1 | 50.00 | 121.00 | 171.00 | OK | |
| r-oldrel-macos-x86_64 | 1.6.1 | 156.00 | 323.00 | 479.00 | OK | |
| r-oldrel-windows-x86_64 | 1.6.1 | 220.00 | 520.00 | 740.00 | OK |
Version: 1.6.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [87s/54s]
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...
> test-basic-fits.R: 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:
> test-basic-fits.R: 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:
> test-basic-fits.R: 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: 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: 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:
> test-basic-fits.R: 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:
> test-basic-fits.R: 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: outer mgc: 10.41538
> test-basic-fits.R: Running sdreport
> 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-basic-fits.R: outer mgc:
> test-basic-fits.R: 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-basic-fits.R: outer mgc: 6253.602
> 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: 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-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: 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-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: 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-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: 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:
> test-basic-fits.R: 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: 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: 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: 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:
> test-basic-fits.R: 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:
> test-basic-fits.R: 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:
> test-basic-fits.R: 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
Saving _problems/test-dsem-35.R
Saving _problems/test-dsem-107.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...
> 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: 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:
> test-basic-fits.R: 0.00454186
> test-basic-fits.R: outer mgc: 0.0009494951
> test-basic-fits.R: outer mgc: 0.0002300872
> test-basic-fits.R: outer mgc: 0.0002300872
> test-basic-fits.R: Running newton_loop #1
> 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: 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
> 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-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 1.567046 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-index-standardization.R: Loading required package: VAST
> test-sfnetworks.R: Linking to GEOS 3.14.1, GDAL 3.13.1, PROJ 9.8.1; sf_use_s2() is TRUE
> 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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.6.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [68s/42s]
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...
> test-basic-fits.R: 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: outer mgc: 8.114833e-05
> test-basic-fits.R: Running newton_loop #1
> 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: 0.2253101
> test-basic-fits.R: outer mgc: 0.001985216
> test-basic-fits.R: outer mgc:
> test-basic-fits.R: 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: outer mgc: 0.03589794
> test-basic-fits.R: outer mgc: 0.03589794
> test-basic-fits.R: Running sdreport
> 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: 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: 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: outer mgc: 10.41538
> test-basic-fits.R: Running sdreport
> 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-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-deviance-residuals.R: Student-t degrees of freedom parameter fixed at 7.81030735915579. To estimate it, set `df = NULL`.
> test-basic-fits.R: Running optimizer_loop #1
> test-deviance-residuals.R: Student-t degrees of freedom parameter fixed at 7.81030735915579. To estimate it, set `df = NULL`.
> test-basic-fits.R: Matching hessian patterns... Done
> test-basic-fits.R: outer mgc: 56569.33
> test-basic-fits.R: outer mgc: 1273
> 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:
> test-basic-fits.R: 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-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: 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: 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
Saving _problems/test-dsem-35.R
Saving _problems/test-dsem-107.R
> 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: 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: outer mgc: 0.0002300872
> test-basic-fits.R: Running newton_loop #1
> 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: 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
> 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-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: 25.44009
> test-basic-fits.R: outer mgc: 7.885275
> test-basic-fits.R: outer mgc:
> test-basic-fits.R: 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: outer mgc: 0.0002300872
> test-basic-fits.R: Running newton_loop #1
> 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: 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:
> test-basic-fits.R: 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-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 1.285941 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-index-standardization.R: Loading required package: VAST
> test-sfnetworks.R: Linking to GEOS 3.14.1, GDAL 3.13.1, PROJ 9.8.1; sf_use_s2() is TRUE
> 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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.6.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [89s/54s]
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...
> test-basic-fits.R: 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:
> test-basic-fits.R: 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: 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: 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:
> test-basic-fits.R: 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: 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-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-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 `d
> test-deviance-residuals.R: f` (e.g., `df = 3`).
> 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-deviance-residuals.R: Student-t degrees of freedom parameter fixed at 7.81030735915579. To estimate it, set `df = NULL`.
> 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:
> test-basic-fits.R: 26004.83
> test-basic-fits.R: outer mgc: 19430.3
> test-basic-fits.R: outer mgc: 5033.068
> test-deviance-residuals.R: Student-t degrees of freedom parameter fixed at 7.81030735915579. To estimate it, set `df = NULL`.
> test-basic-fits.R: outer mgc: 2810.923
> test-basic-fits.R: outer mgc: 474.8056
> test-basic-fits.R: outer mgc:
> test-basic-fits.R: 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-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: 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: 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:
> test-basic-fits.R: 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
Saving _problems/test-dsem-35.R
Saving _problems/test-dsem-107.R
> 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:
> test-basic-fits.R: 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: 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
> test-basic-fits.R: outer mgc: 0.0006480273
> test-basic-fits.R: outer mgc: 0.0006480273
> test-basic-fits.R: outer mgc:
> test-basic-fits.R: 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-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: 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: outer mgc: 0.0002300872
> test-basic-fits.R: Running newton_loop #1
> 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: 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
> 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-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 1.718141 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-index-standardization.R: Loading required package: VAST
> test-sfnetworks.R: Linking to GEOS 3.14.1, GDAL 3.13.1, PROJ 9.8.1; sf_use_s2() is TRUE
> 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
Flavor: r-patched-linux-x86_64
Version: 1.6.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [91s/55s]
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...
> test-basic-fits.R: 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:
> test-basic-fits.R: 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: 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-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-deviance-residuals.R: Student-t degrees of freedom parameter fixed at 7.81030735915579. To estimate it, set `df = NULL`.
> 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-deviance-residuals.R: Student-t degrees of freedom parameter fixed at 7.81030735915579. To estimate it, set `df = NULL`.
> test-basic-fits.R: outer mgc:
> test-basic-fits.R: 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-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-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: 626.5097
> test-basic-fits.R: outer mgc: 1218.44
> test-basic-fits.R: outer mgc:
> test-basic-fits.R: 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: 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-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:
> test-basic-fits.R: 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: 5033.068
Saving _problems/test-dsem-35.R
Saving _problems/test-dsem-107.R
> 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:
> test-basic-fits.R: 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: 243.2674
> test-basic-fits.R: outer mgc:
> test-basic-fits.R: 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:
> test-basic-fits.R: 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-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: 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: 0.0002300872
> test-basic-fits.R: outer mgc: 0.0002300872
> test-basic-fits.R: Running newton_loop #1
> test-basic-fits.R: outer mgc:
> test-basic-fits.R: 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: 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
> test-basic-fits.R: outer mgc: 0.0006480273
> test-basic-fits.R: outer mgc: 0.0006480273
> test-basic-fits.R: outer mgc:
> test-basic-fits.R: 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-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:
> test-basic-fits.R: 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:
> test-basic-fits.R: 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:
> test-basic-fits.R: 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
> test-basic-fits.R: outer mgc: 0.0006480273
> test-basic-fits.R: outer mgc: 0.0006480273
> test-basic-fits.R: outer mgc:
> test-basic-fits.R: 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 1.720469 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
Flavor: r-release-linux-x86_64
Version: 1.6.1
Check: package dependencies
Result: ERROR
Package required and available but unsuitable version: ‘dsem’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-release-macos-x86_64
Version: 1.6.0
Check: tests
Result: ERROR
Running 'testthat.R' [50s]
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...
> test-basic-fits.R: 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: 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: 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: 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: 0.02246359
> test-basic-fits.R: outer mgc: 0.0003993413
> test-basic-fits.R: Running newton_loop #1
> test-basic-fits.R: outer mgc: 0.0003993413
> test-basic-fits.R: outer mgc: 10.41578
> test-basic-fits.R: outer mgc: 10.41499
> test-basic-fits.R: Running sdreport
> 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: 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: 1.2346e-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-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-deviance-residuals.R: Student-t degrees of freedom parameter fixed at 7.8103073591526. To estimate it, set `df = NULL`.
> test-basic-fits.R: Running optimizer_loop #1
> test-deviance-residuals.R: Student-t degrees of freedom parameter fixed at 7.8103073591526. To estimate it, set `df = NULL`.
> 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: 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: 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: 0.02246359
> test-basic-fits.R: outer mgc: 0.0003993413
> test-basic-fits.R: Running newton_loop #1
> 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: 0.0003993413
> 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-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: 1.2346e-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
Saving _problems/test-dsem-35.R
Saving _problems/test-dsem-107.R
> 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: 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: 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
> 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-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: 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: 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
> 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 3.12.1, PROJ 9.7.1; sf_use_s2() is TRUE
> 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 1.554214 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-index-standardization.R: Loading required package: VAST
> test-sfnetworks.R: Linking to GEOS 3.14.1, GDAL 3.12.1, PROJ 9.7.1; sf_use_s2() is TRUE
> 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
Flavor: r-release-windows-x86_64