Last updated on 2026-06-16 13:56:01 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.6.0 | 223.94 | 572.01 | 795.95 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.6.0 | 206.58 | 463.50 | 670.08 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.6.0 | 300.00 | 849.93 | 1149.93 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.6.0 | 404.00 | 607.20 | 1011.20 | ERROR | |
| r-devel-windows-x86_64 | 1.6.0 | 241.00 | 630.00 | 871.00 | OK | |
| r-patched-linux-x86_64 | 1.6.0 | 272.55 | 600.01 | 872.56 | OK | |
| r-release-linux-x86_64 | 1.6.0 | 264.58 | 578.74 | 843.32 | OK | |
| r-release-macos-arm64 | 1.6.0 | 54.00 | 137.00 | 191.00 | OK | |
| r-release-macos-x86_64 | 1.6.0 | 160.00 | 100.00 | 260.00 | ERROR | |
| r-release-windows-x86_64 | 1.6.0 | 244.00 | 619.00 | 863.00 | OK | |
| r-oldrel-macos-arm64 | 1.6.0 | 55.00 | 138.00 | 193.00 | OK | |
| r-oldrel-macos-x86_64 | 1.6.0 | 148.00 | 331.00 | 479.00 | OK | |
| r-oldrel-windows-x86_64 | 1.6.0 | 316.00 | 792.00 | 1108.00 | OK |
Version: 1.6.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [82s/48s]
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: 139.7797
> test-basic-fits.R: outer mgc: 50.0056
> test-basic-fits.R: outer mgc: 10.49566
> test-basic-fits.R: outer mgc: 42.55798
> test-basic-fits.R: outer mgc: 33.025
> test-basic-fits.R: outer mgc: 66.66318
> test-basic-fits.R: outer mgc: 14.40933
> test-basic-fits.R: outer mgc: 16.20354
> test-basic-fits.R: outer mgc: 6.049868
> test-basic-fits.R: outer mgc: 10.16643
> test-basic-fits.R: outer mgc: 6.303317
> test-basic-fits.R: outer mgc: 3.01656
> test-basic-fits.R: outer mgc: 8.557232
> test-basic-fits.R: outer mgc: 2.408678
> test-basic-fits.R: outer mgc: 0.09609061
> test-basic-fits.R: outer mgc: 0.02084409
> test-basic-fits.R: outer mgc: 0.02100457
> test-basic-fits.R: outer mgc: 3.435621e-05
> test-basic-fits.R: outer mgc: 8.373763e-07
> test-basic-fits.R: Running newton_loop #1
> test-basic-fits.R: outer mgc: 8.373763e-07
> test-basic-fits.R: outer mgc: 0.03589508
> test-basic-fits.R: outer mgc: 0.03589548
> test-basic-fits.R: outer mgc: 0.2249867
> test-basic-fits.R: outer mgc: 0.2253945
> test-basic-fits.R: outer mgc: 0.001990324
> test-basic-fits.R: outer mgc: 0.001989592
> test-basic-fits.R: outer mgc: 0.6192716
> test-basic-fits.R: outer mgc: 0.6193904
> test-basic-fits.R: outer mgc: 0.1341367
> test-basic-fits.R: outer mgc: 0.1342761
> test-basic-fits.R: Running sdreport
> test-basic-fits.R: outer mgc: 0.03589528
> test-basic-fits.R: outer mgc: 0.03589528
> test-basic-fits.R: outer mgc: 0.2249863
> test-basic-fits.R: outer mgc: 0.2253948
> test-basic-fits.R: outer mgc: 0.001990341
> test-basic-fits.R: outer mgc: 0.001989574
> test-basic-fits.R: outer mgc: 0.6192713
> test-basic-fits.R: outer mgc: 0.6193908
> test-basic-fits.R: outer mgc: 0.1341364
> test-basic-fits.R: outer mgc: 0.1342765
> test-basic-fits.R: outer mgc: 8.373763e-07
> 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: 56573.54
> test-basic-fits.R: outer mgc: 1272.962
> test-basic-fits.R: outer mgc: 24819.95
> test-basic-fits.R: outer mgc: 26007.69
> test-basic-fits.R: outer mgc: 19429.4
> test-basic-fits.R: outer mgc: 5031.503
> test-basic-fits.R: outer mgc: 2811.473
> test-basic-fits.R: outer mgc: 475.8342
> test-basic-fits.R: outer mgc: 6192.112
> test-basic-fits.R: outer mgc: 5542.985
> test-basic-fits.R: outer mgc: 61.50294
> test-basic-fits.R: outer mgc: 2566.65
> test-basic-fits.R: outer mgc: 634.0082
> test-basic-fits.R: outer mgc: 1073.525
> test-basic-fits.R: outer mgc: 631.7263
> test-basic-fits.R: outer mgc: 597.6543
> test-basic-fits.R: outer mgc: 2471.182
> test-basic-fits.R: outer mgc: 433.9127
> test-basic-fits.R: outer mgc: 4514.008
> test-basic-fits.R: outer mgc: 4085.049
> test-basic-fits.R: outer mgc: 1283.438
> test-basic-fits.R: outer mgc: 326.7172
> test-basic-fits.R: outer mgc: 92.07726
> test-basic-fits.R: outer mgc: 12.53704
> test-basic-fits.R: outer mgc: 4.53008
> test-basic-fits.R: outer mgc: 0.1280528
> test-basic-fits.R: outer mgc: 0.04303635
> test-basic-fits.R: outer mgc: 0.0197487
> test-basic-fits.R: Running newton_loop #1
> test-basic-fits.R: outer mgc: 0.0197487
> test-basic-fits.R: outer mgc: 10.43484
> test-basic-fits.R: outer mgc: 10.39534
> test-basic-fits.R: outer mgc: 420.1428
> test-basic-fits.R: outer mgc: 420.1033
> test-basic-fits.R: outer mgc: 4715.533
> test-basic-fits.R: outer mgc: 4715.494
> test-basic-fits.R: outer mgc: 47003.36
> test-basic-fits.R: outer mgc: 47003.32
> test-basic-fits.R: outer mgc: 0.4212049
> test-basic-fits.R: outer mgc: 0.462247
> test-basic-fits.R: outer mgc: 0.6366283
> test-basic-fits.R: outer mgc: 0.637081
> test-basic-fits.R: outer mgc: 0.4781679
> test-basic-fits.R: outer mgc: 0.4367504
> test-basic-fits.R: outer mgc: 10.41513
> test-basic-fits.R: outer mgc: 10.41513
> test-basic-fits.R: outer mgc: 420.1231
> test-basic-fits.R: outer mgc: 420.1231
> test-basic-fits.R: outer mgc: 4715.514
> test-basic-fits.R: outer mgc: 4715.514
> test-basic-fits.R: outer mgc: 47003.34
> test-basic-fits.R: outer mgc: 47003.34
> test-basic-fits.R: outer mgc: 0.4409389
> test-basic-fits.R: outer mgc: 0.4424835
> test-basic-fits.R: outer mgc: 0.6367749
> test-basic-fits.R: outer mgc: 0.6369318
> test-basic-fits.R: outer mgc: 0.4584172
> test-basic-fits.R: outer mgc: 0.4564972
> test-basic-fits.R: outer mgc: 1.654217e-08
> test-basic-fits.R: Running sdreport
> 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-basic-fits.R: Matching hessian patterns...
> test-deviance-residuals.R: Student-t degrees of freedom parameter fixed at 7.81030735915579. To estimate it, set `df = NULL`.
> test-basic-fits.R: Done
> test-basic-fits.R: outer mgc: 56573.54
> test-basic-fits.R: outer mgc: 1272.962
> test-basic-fits.R: outer mgc: 24819.95
> test-basic-fits.R: outer mgc: 26007.69
> 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: 19429.4
> test-basic-fits.R: outer mgc: 5031.503
> test-basic-fits.R: outer mgc: 2811.473
> test-basic-fits.R: outer mgc: 475.8342
> test-basic-fits.R: outer mgc: 6192.112
> test-basic-fits.R: outer mgc: 5542.985
> test-basic-fits.R: outer mgc: 61.50294
> test-basic-fits.R: outer mgc: 2566.65
> 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: 634.0082
> test-basic-fits.R: outer mgc: 1073.525
> test-basic-fits.R: outer mgc: 631.7263
> test-basic-fits.R: outer mgc: 597.6543
> test-basic-fits.R: outer mgc: 2471.182
> test-basic-fits.R: outer mgc: 433.9127
> test-basic-fits.R: outer mgc: 4514.008
> test-basic-fits.R: outer mgc: 4085.049
> test-basic-fits.R: outer mgc: 1283.438
> test-basic-fits.R: outer mgc: 326.7172
> test-basic-fits.R: outer mgc: 92.07726
> test-basic-fits.R: outer mgc: 12.53704
> test-basic-fits.R: outer mgc: 4.53008
> test-basic-fits.R: outer mgc: 0.1280528
> test-basic-fits.R: outer mgc: 0.04303635
> test-basic-fits.R: outer mgc: 0.0197487
> test-basic-fits.R: Running newton_loop #1
> test-basic-fits.R: outer mgc: 0.0197487
> test-basic-fits.R: outer mgc: 10.43484
> test-basic-fits.R: outer mgc: 10.39534
> test-basic-fits.R: outer mgc: 420.1428
> test-basic-fits.R: outer mgc: 420.1033
> test-basic-fits.R: outer mgc: 4715.533
> test-basic-fits.R: outer mgc: 4715.494
> test-basic-fits.R: outer mgc: 47003.36
> test-basic-fits.R: outer mgc: 47003.32
> test-basic-fits.R: outer mgc: 0.4212049
> test-basic-fits.R: outer mgc: 0.462247
> test-basic-fits.R: outer mgc: 0.6366283
> test-basic-fits.R: outer mgc: 0.637081
> test-basic-fits.R: outer mgc: 0.4781679
> test-basic-fits.R: outer mgc: 0.4367504
> test-basic-fits.R: Running sdreport
> test-basic-fits.R: outer mgc: 10.41513
> test-basic-fits.R: outer mgc: 10.41513
> test-basic-fits.R: outer mgc: 420.1231
> test-basic-fits.R: outer mgc: 420.1231
> test-basic-fits.R: outer mgc: 4715.514
> test-basic-fits.R: outer mgc: 4715.514
> test-basic-fits.R: outer mgc: 47003.34
> test-basic-fits.R: outer mgc: 47003.34
> test-basic-fits.R: outer mgc: 0.4409389
> test-basic-fits.R: outer mgc: 0.4424835
> test-basic-fits.R: outer mgc: 0.6367749
> test-basic-fits.R: outer mgc: 0.6369318
> test-basic-fits.R: outer mgc: 0.4584172
> test-basic-fits.R: outer mgc: 0.4564972
> test-basic-fits.R: outer mgc: 1.654217e-08
> 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: 329.6031
> test-basic-fits.R: outer mgc: 68.05233
> test-basic-fits.R: outer mgc: 18.19656
> test-basic-fits.R: outer mgc: 29.92053
> test-basic-fits.R: outer mgc: 43.10927
> test-basic-fits.R: outer mgc: 37.2851
> test-basic-fits.R: outer mgc: 39.29585
> test-basic-fits.R: outer mgc: 13.80125
> test-basic-fits.R: outer mgc: 56.22918
> test-basic-fits.R: outer mgc: 25.52038
> test-basic-fits.R: outer mgc: 7.92955
> test-basic-fits.R: outer mgc: 4.087912
> test-basic-fits.R: outer mgc: 3.712102
> test-basic-fits.R: outer mgc: 0.7345282
> test-basic-fits.R: outer mgc: 0.1433986
> test-basic-fits.R: outer mgc: 0.06908389
> test-basic-fits.R: outer mgc: 0.004477842
> test-basic-fits.R: outer mgc: 0.0009683881
> test-basic-fits.R: outer mgc: 0.0002287949
> test-basic-fits.R: Running newton_loop #1
> test-basic-fits.R: outer mgc: 0.0002287949
> test-basic-fits.R: outer mgc: 0.03431302
> test-basic-fits.R: outer mgc: 0.03422994
> test-basic-fits.R: outer mgc: 0.0006446274
> test-basic-fits.R: outer mgc: 0.0006324006
> test-basic-fits.R: outer mgc: 0.0006470594
> test-basic-fits.R: outer mgc: 0.0006489578
> test-basic-fits.R: outer mgc: 0.0006101428
> test-basic-fits.R: outer mgc: 0.0006186895
> test-basic-fits.R: outer mgc: 0.222149
> test-basic-fits.R: outer mgc: 0.2229985
> test-basic-fits.R: outer mgc: 0.6365467
> test-basic-fits.R: outer mgc: 0.6371612
> test-basic-fits.R: outer mgc: 0.1350688
> test-basic-fits.R: outer mgc: 0.1356611
> test-basic-fits.R: Running sdreport
> test-basic-fits.R: outer mgc: 0.0342717
> test-basic-fits.R: outer mgc: 0.0342717
> test-basic-fits.R: outer mgc: 0.0006385136
> test-basic-fits.R: outer mgc: 0.0006385136
> test-basic-fits.R: outer mgc: 0.0006480083
> test-basic-fits.R: outer mgc: 0.0006480082
> test-basic-fits.R: outer mgc: 0.0006144158
> test-basic-fits.R: outer mgc: 0.0006144158
> test-basic-fits.R: outer mgc: 0.222378
> test-basic-fits.R: outer mgc: 0.2227699
> test-basic-fits.R: outer mgc: 0.6367749
> test-basic-fits.R: outer mgc: 0.6369318
> test-basic-fits.R: outer mgc: 0.1352972
> test-basic-fits.R: outer mgc: 0.1354319
> test-basic-fits.R: outer mgc: 7.35002e-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: 329.6031
> test-basic-fits.R: outer mgc: 68.05233
> test-basic-fits.R: outer mgc: 18.19656
> test-basic-fits.R: outer mgc: 29.92053
> test-basic-fits.R: outer mgc: 43.10927
> test-basic-fits.R: outer mgc: 37.2851
> test-basic-fits.R: outer mgc: 39.29585
> test-basic-fits.R: outer mgc: 13.80125
> test-basic-fits.R: outer mgc: 56.22918
> test-basic-fits.R: outer mgc: 25.52038
> test-basic-fits.R: outer mgc: 7.92955
> test-basic-fits.R: outer mgc: 4.087912
> test-basic-fits.R: outer mgc: 3.712102
> test-basic-fits.R: outer mgc: 0.7345282
> test-basic-fits.R: outer mgc: 0.1433986
> test-basic-fits.R: outer mgc: 0.06908389
> test-basic-fits.R: outer mgc: 0.004477842
> test-basic-fits.R: outer mgc: 0.0009683881
> test-basic-fits.R: outer mgc: 0.0002287949
> test-basic-fits.R: Running newton_loop #1
> test-basic-fits.R: outer mgc: 0.0002287949
> test-basic-fits.R: outer mgc: 0.03431302
> test-basic-fits.R: outer mgc: 0.03422994
> test-basic-fits.R: outer mgc: 0.0006446274
> test-basic-fits.R: outer mgc: 0.0006324006
> test-basic-fits.R: outer mgc: 0.0006470594
> test-basic-fits.R: outer mgc: 0.0006489578
> test-basic-fits.R: outer mgc: 0.0006101428
> test-basic-fits.R: outer mgc: 0.0006186895
> test-basic-fits.R: outer mgc: 0.222149
> test-basic-fits.R: outer mgc: 0.2229985
> test-basic-fits.R: outer mgc: 0.6365467
> test-basic-fits.R: outer mgc: 0.6371612
> test-basic-fits.R: outer mgc: 0.1350688
> test-basic-fits.R: outer mgc: 0.1356611
> test-basic-fits.R: Running sdreport
> test-basic-fits.R: outer mgc: 0.0342717
> test-basic-fits.R: outer mgc: 0.0342717
> test-basic-fits.R: outer mgc: 0.0006385136
> test-basic-fits.R: outer mgc: 0.0006385136
> test-basic-fits.R: outer mgc: 0.0006480083
> test-basic-fits.R: outer mgc: 0.0006480082
> test-basic-fits.R: outer mgc: 0.0006144158
> test-basic-fits.R: outer mgc: 0.0006144158
> test-basic-fits.R: outer mgc: 0.222378
> test-basic-fits.R: outer mgc: 0.2227699
> test-basic-fits.R: outer mgc: 0.6367749
> test-basic-fits.R: outer mgc: 0.6369318
> test-basic-fits.R: outer mgc: 0.1352972
> test-basic-fits.R: outer mgc: 0.1354319
> test-basic-fits.R: outer mgc: 7.35002e-10
> test-mesh.R: Linking to GEOS 3.13.0, GDAL 3.10.3, PROJ 9.6.2; 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 2.073942 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 0.0008856969 0.1179880
> test-platform.R: theta_z 1.0051426964 0.1053589
> test-platform.R: log_lambda -2.4633570302 0.6907046
> test-platform.R: log_sigma -0.2413211707 0.1593839
> test-platform.R: log_kappa 0.1658324137 0.2109340
> test-platform.R: Maximum gradient component: 7.768524e-05
> test-platform.R:
> test-platform.R: Proportion conditional deviance explained:
> test-platform.R: [1] 0.869631
> 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> 1.005143 0.1053589 9.540183 1.425808e-21
> test-platform.R:
> test-platform.R: Fixed terms:
> test-platform.R: Estimate Std_Error z_value p_value
> test-platform.R: (Intercept) 0.0008856969 0.117988 0.007506668 0.9940106
> 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-devel-linux-x86_64-fedora-gcc
Version: 1.6.0
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-release-macos-x86_64