CRAN Package Check Results for Package tinyVAST

Last updated on 2026-11-03 02:54:11 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.6.3 242.65 328.80 571.45 OK
r-devel-linux-x86_64-debian-gcc 1.6.3 199.81 259.42 459.23 OK
r-devel-linux-x86_64-fedora-clang 1.6.3 138.00 204.56 342.56 ERROR
r-devel-linux-x86_64-fedora-gcc 1.6.3 269.00 239.99 508.99 OK
r-devel-windows-x86_64 1.6.3 256.00 472.00 728.00 OK
r-patched-linux-x86_64 1.6.3 284.67 333.02 617.69 OK
r-release-linux-x86_64 1.6.3 268.47 332.83 601.30 OK
r-release-macos-arm64 1.6.3 57.00 76.00 133.00 OK
r-release-macos-x86_64 1.6.3 171.00 168.00 339.00 OK
r-release-windows-x86_64 1.6.3 258.00 355.00 613.00 OK
r-oldrel-macos-arm64 1.6.3 OK
r-oldrel-macos-x86_64 1.6.3 159.00 180.00 339.00 OK
r-oldrel-windows-x86_64 1.6.3 348.00 449.00 797.00 OK

Check Details

Version: 1.6.3
Check: tests
Result: ERROR Running ‘testthat.R’ [52s/30s] 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: 0.03511878 > test-basic-fits.R: outer mgc: 0.01736614 > test-basic-fits.R: outer mgc: 0.0009654501 > test-basic-fits.R: outer mgc: 8.114827e-05 > test-basic-fits.R: Running newton_loop #1 > test-basic-fits.R: outer mgc: 8.114827e-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: 1.683643e-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-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: 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-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: 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-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: 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: 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-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: 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: 1.373289e-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: 24820.02 > test-basic-fits.R: outer mgc: 26004.83 > test-basic-fits.R: outer mgc: 19430.3 > test-dsem.R: Read 1 record > 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: List of estimated fixed and random effects: > test-basic-fits.R: outer mgc: 626.5097 > test-dsem.R: Coefficient_name Number_of_coefficients Type > test-dsem.R: 1 beta_z 3 Fixed > test-dsem.R: 2 mu_j 2 Fixed > test-dsem.R: 3 x_tj 200 Random > test-dsem.R: Running nlminb_loop #1 > test-basic-fits.R: outer mgc: 1218.44 > test-basic-fits.R: outer mgc: 657.8356 > test-dsem.R: Running newton_loop #1 > 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: 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: 1.373289e-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-dsem.R: Read 1 record > 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-dsem.R: List of estimated fixed and random effects: > test-dsem.R: Coefficient_name Number_of_coefficients Type > test-dsem.R: 1 beta_z 3 Fixed > test-dsem.R: 2 mu_j 2 Fixed > test-dsem.R: 3 x_tj 200 Random > test-dsem.R: Running nlminb_loop #1 > 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-dsem.R: Running newton_loop #1 > 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: 7.676489e-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: 7.676489e-10 > test-mesh.R: Linking to GEOS 3.14.1, GDAL 3.12.4, 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 1.05614 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-sfnetworks.R: Linking to GEOS 3.14.1, GDAL 3.12.4, 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 Saving _problems/test-smooths-129.R [ FAIL 1 | WARN 0 | SKIP 21 | PASS 116 ] ══ Skipped tests (21) ══════════════════════════════════════════════════════════ • On CRAN (20): '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-basic-fits.R:142:3', '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' • {VAST} is not installed (1): 'test-index-standardization.R:77:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-smooths.R:125:3'): ti and te splines work ────────────────────── Error in `nlminb(start = opt$par, objective = obj$fn, gradient = obj$gr, control = list(eval.max = control$eval.max, iter.max = control$iter.max, trace = control$trace))`: NA/NaN gradient evaluation Backtrace: ▆ 1. └─tinyVAST::tinyVAST(form, data = dat, control = tinyVASTcontrol(getsd = FALSE)) at test-smooths.R:125:3 2. └─tinyVAST (local) run_optimizer(obj, control) 3. ├─base::suppressWarnings(...) 4. │ └─base::withCallingHandlers(...) 5. └─stats::nlminb(...) [ FAIL 1 | WARN 0 | SKIP 21 | PASS 116 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang