R Under development (unstable) (2025-11-25 r89063 ucrt) -- "Unsuffered Consequences"
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> options(Matrix.warnDeprecatedCoerce = 2)
> 
> library(testthat)
> library(sdmTMB)
> 
> test_check("sdmTMB")
Starting 2 test processes.
> test-3-families.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-3-families.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-3-families.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.R: Loading required package: nlme
> test-deviance.R: This is mgcv 1.9-4. For overview type '?mgcv'.
> test-emmeans.R: Welcome to emmeans.
> test-emmeans.R: Caution: You lose important information if you filter this package's results.
> test-emmeans.R: See '? untidy'
> test-emmeans.R: NOTE: Results may be misleading due to involvement in interactions
> test-extra-time.R: Detected irregular time spacing with an AR(1) or random walk process.
> test-extra-time.R: Consider filling in the missing time slices with `extra_time`.
> test-extra-time.R: `extra_time = c(2006, 2008, 2010, 2012, 2014, 2016)`
[ FAIL 0 | WARN 0 | SKIP 237 | PASS 275 ]

══ Skipped tests (237) ═════════════════════════════════════════════════════════
• On CRAN (237): 'test-1-visreg.R:2:3', 'test-1-visreg.R:189:3',
  'test-2-fit-less-basic.R:2:3', 'test-2-fit-less-basic.R:32:3',
  'test-2-fit-less-basic.R:84:3', 'test-2-fit-less-basic.R:100:3',
  'test-2-fit-less-basic.R:171:3', 'test-2-fit-less-basic.R:189:3',
  'test-2-fit-less-basic.R:239:3', 'test-2-fit-less-basic.R:247:3',
  'test-2-fit-less-basic.R:276:3', 'test-2-fit-less-basic.R:294:3',
  'test-2-fit-less-basic.R:317:3', 'test-2-fit-less-basic.R:361:3',
  'test-2-fit-less-basic.R:372:3', 'test-2-fit-less-basic.R:426:3',
  'test-2-fit-less-basic.R:501:3', 'test-2-print-anisotropy.R:2:3',
  'test-2-tidy.R:2:3', 'test-2-tidy.R:17:3', 'test-2-tidy.R:33:3',
  'test-2-tidy.R:48:3', 'test-2-tidy.R:61:3', 'test-2-tidy.R:83:3',
  'test-2-tidy.R:96:3', 'test-2-tidy.R:113:3', 'test-2-tidy.R:148:3',
  'test-2-tidy.R:189:3', 'test-2-tidy.R:219:3', 'test-3-families.R:39:3',
  'test-3-families.R:59:3', 'test-3-families.R:136:3',
  'test-3-families.R:155:3', 'test-3-families.R:170:3',
  'test-3-families.R:205:3', 'test-3-families.R:219:3',
  'test-3-families.R:232:3', 'test-3-families.R:249:3',
  'test-3-families.R:272:3', 'test-3-families.R:504:3',
  'test-3-families.R:548:3', 'test-3-spatial-varying.R:2:3',
  'test-3-spatial-varying.R:94:3', 'test-3-spatial-varying.R:119:3',
  'test-3-spatial-varying.R:139:3', 'test-4-index-calculation.R:3:3',
  'test-4-index-calculation.R:58:3', 'test-4-index-calculation.R:85:3',
  'test-5-residuals.R:20:3', 'test-5-residuals.R:286:3',
  'test-5-residuals.R:387:3', 'test-5-residuals.R:400:3',
  'test-5-residuals.R:440:3', 'test-5-residuals.R:459:3',
  'test-6-tmb-simulation.R:2:3', 'test-6-tmb-simulation.R:34:3',
  'test-6-tmb-simulation.R:69:3', 'test-6-tmb-simulation.R:121:3',
  'test-6-tmb-simulation.R:163:3', 'test-6-tmb-simulation.R:184:3',
  'test-6-tmb-simulation.R:259:3', 'test-8-delta2.R:2:3',
  'test-8-delta2.R:77:3', 'test-8-delta2.R:146:3', 'test-8-delta2.R:252:3',
  'test-8-delta2.R:346:3', 'test-8-delta2.R:425:3', 'test-8-delta2.R:474:3',
  'test-9-mvn-simulation.R:2:3', 'test-9-mvn-simulation.R:26:3',
  'test-9-mvn-simulation.R:51:3', 'test-9-mvn-simulation.R:134:3',
  'test-9-mvn-simulation.R:159:3', 'test-9-mvn-simulation.R:232:3',
  'test-9-mvn-simulation.R:307:3', 'test-aniso-plots.R:2:3',
  'test-betabinomial.R:19:3', 'test-betabinomial.R:58:3',
  'test-betabinomial.R:91:3', 'test-betabinomial.R:125:3',
  'test-betabinomial.R:162:3', 'test-cAIC.R:2:3', 'test-collapse.R:2:3',
  'test-collapse.R:86:3', 'test-cross-validation.R:3:3',
  'test-cross-validation.R:52:3', 'test-cross-validation.R:70:3',
  'test-cross-validation.R:98:3', 'test-cross-validation.R:148:3',
  'test-cross-validation.R:170:3', 'test-cross-validation.R:308:3',
  'test-cross-validation.R:336:3', 'test-cross-validation.R:442:3',
  'test-cross-validation.R:502:3', 'test-cross-validation.R:552:3',
  'test-cross-validation.R:588:3', 'test-cross-validation.R:610:3',
  'test-cross-validation.R:633:3', 'test-delta-population-predictions.R:2:3',
  'test-delta.R:6:3', 'test-delta.R:51:3', 'test-delta.R:63:3',
  'test-delta.R:81:3', 'test-delta.R:95:3', 'test-delta.R:109:3',
  'test-delta.R:122:3', 'test-delta.R:181:3', 'test-delta.R:226:3',
  'test-deprecated-args.R:2:3', 'test-deprecated-args.R:65:3',
  'test-dharma.R:2:3', 'test-extra-optimization.R:2:3',
  'test-extra-time.R:3:3', 'test-extra-time.R:45:3', 'test-extra-time.R:119:3',
  'test-extra-time.R:183:3', 'test-extra-time.R:208:3',
  'test-factor-levels.R:2:3', 'test-factor-levels.R:36:3',
  'test-factor-levels.R:89:3', 'test-forecasting.R:2:3',
  'test-ggeffect.R:161:3', 'test-index.R:2:3', 'test-index.R:66:3',
  'test-index.R:117:3', 'test-index.R:150:3', 'test-index.R:237:3',
  'test-index.R:278:3', 'test-index.R:314:3', 'test-link-prediction.R:5:3',
  'test-link-prediction.R:66:3', 'test-links.R:2:3', 'test-methods.R:2:3',
  'test-methods.R:32:3', 'test-methods.R:46:3', 'test-methods.R:86:3',
  'test-mix.R:2:3', 'test-mix.R:60:3', 'test-mix.R:75:3', 'test-mix.R:93:3',
  'test-mix.R:112:3', 'test-mix.R:173:3', 'test-nonstationary.R:116:3',
  'test-nonstationary.R:161:3', 'test-nonstationary.R:207:3',
  'test-nonstationary.R:234:3', 'test-nonstationary.R:285:3',
  'test-offset.R:2:3', 'test-offset.R:19:3', 'test-offset.R:79:3',
  'test-offset.R:98:3', 'test-offset.R:143:3', 'test-offset.R:165:3',
  'test-parameter-bounds.R:11:3', 'test-1-fit-basic.R:128:3',
  'test-1-fit-basic.R:177:3', 'test-1-fit-basic.R:219:3',
  'test-poisson-link.R:2:3', 'test-prediction-missing-years.R:2:3',
  'test-projection.R:2:3', 'test-projection.R:126:3',
  'test-projection.R:172:3', 'test-projection.R:218:3', 'test-priors.R:22:3',
  'test-priors.R:123:3', 'test-priors.R:170:3',
  'test-random-intercepts.R:11:3', 'test-random-intercepts.R:146:3',
  'test-random-intercepts.R:181:3', 'test-random-intercepts.R:247:3',
  'test-random-intercepts.R:285:3', 'test-range-edge.R:2:3',
  'test-range-edge.R:37:3', 'test-range-edge.R:64:3',
  'test-range-edge.R:103:3', 'test-range-edge.R:157:3',
  'test-range-edge.R:181:3', 'test-range-edge.R:207:3',
  'test-range-edge.R:231:3', 'test-range-edge.R:263:3',
  'test-range-edge.R:284:3', 'test-reml.R:2:3', 'test-reml.R:75:3',
  'test-sanity.R:2:3', 'test-sdmTMB-simulate.R:2:3', 'test-smooths.R:4:3',
  'test-smooths.R:15:3', 'test-smooths.R:50:3', 'test-smooths.R:90:3',
  'test-smooths.R:127:3', 'test-smooths.R:203:3', 'test-smooths.R:253:3',
  'test-smooths.R:275:3', 'test-smooths.R:297:3', 'test-smooths.R:317:3',
  'test-smooths.R:338:3', 'test-smooths.R:358:3', 'test-smooths.R:374:3',
  'test-smooths.R:390:3', 'test-smooths.R:406:3', 'test-smooths.R:422:3',
  'test-smooths.R:432:3', 'test-smooths.R:448:3', 'test-smooths.R:465:3',
  'test-smooths.R:480:3', 'test-threshold-models.R:2:3',
  'test-threshold-models.R:17:3', 'test-threshold-models.R:30:3',
  'test-time-varying.R:2:3', 'test-time-varying.R:148:3',
  'test-tmb-simulation.R:2:3', 'test-tmb-simulation.R:34:3',
  'test-tmb-simulation.R:71:3', 'test-tmb-simulation.R:121:3',
  'test-tmb-simulation.R:157:3', 'test-tmb-simulation.R:199:3',
  'test-tmb-simulation.R:245:3', 'test-tmb-simulation.R:294:3',
  'test-tmb-simulation.R:312:3', 'test-tmb-simulation.R:358:3',
  'test-tmb-simulation.R:421:3', 'test-random-effects.R:14:3',
  'test-random-effects.R:281:3', 'test-random-effects.R:316:3',
  'test-random-effects.R:381:3', 'test-random-effects.R:418:3',
  'test-truncated-dists.R:2:3', 'test-truncated-dists.R:41:3',
  'test-truncated-dists.R:80:3', 'test-truncated-dists.R:105:3',
  'test-truncated-dists.R:130:3', 'test-utm-conversions.R:2:3',
  'test-waywiser.R:2:3', 'test-waywiser.R:41:3', 'test-waywiser.R:71:3',
  'test-waywiser.R:95:3', 'test-without-spatial.R:2:3'

[ FAIL 0 | WARN 0 | SKIP 237 | PASS 275 ]
> 
> proc.time()
   user  system elapsed 
  11.95    0.53   38.70