* using log directory ‘/Users/ripley/R/packages/tests-devel/ngme2.Rcheck’ * using R Under development (unstable) (2026-08-31 r90454) * using platform: aarch64-apple-darwin25.6.0 * R was compiled by Apple clang version 21.0.0 (clang-2100.1.1.101) GNU Fortran (GCC) 14.2.0 * running under: macOS Tahoe 26.6.2 * using session charset: UTF-8 * current time: 2026-08-31 17:19:15 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘ngme2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ngme2’ version ‘0.9.8’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ngme2’ can be installed ... [131s/87s] OK * used C++ compiler: ‘Apple clang version 21.0.0 (clang-2100.1.1.101)’ * used SDK: ‘MacOSX26.5.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [11s/11s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [55s/55s] [55s/55s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > > test_check("ngme2") Loading required package: ngme2 This is ngme2 of version 0.9.8 - See our homepage: https://davidbolin.github.io/ngme2 for more details. Attaching package: 'ngme2' The following object is masked from 'package:stats': ar List of 6 $ mean : num [1:3] -1.746 0.737 -2.318 $ sd : num [1:3] 0.647 0.738 0.784 $ 0.05q : num [1:3] -2.824 -0.358 -3.611 $ 0.95q : num [1:3] -0.722 2.049 -1.002 $ median: num [1:3] -1.706 0.662 -2.319 $ mode : num [1:3] -1.5 0.5 -2.3 - attr(*, "samples")= num [1:10, 1:500] -1.863 -1.851 -1.237 0.762 3.911 ... Starting estimation... iteration = : 1 grad.norm() = 508.192 pflug_sum = 0, max_pflug_sum = 0 --------------------------- iteration = : 2 grad.norm() = 495.494 pflug_sum = 251474, max_pflug_sum = 251474 --------------------------- iteration = : 3 grad.norm() = 471.659 pflug_sum = 484088, max_pflug_sum = 484088 --------------------------- iteration = : 4 grad.norm() = 443.693 pflug_sum = 692515, max_pflug_sum = 692515 --------------------------- iteration = : 5 grad.norm() = 427.568 pflug_sum = 880816, max_pflug_sum = 880816 --------------------------- iteration = : 6 grad.norm() = 393.635 pflug_sum = 1.0483e+06, max_pflug_sum = 1.0483e+06 --------------------------- iteration = : 7 grad.norm() = 367.389 pflug_sum = 1.19248e+06, max_pflug_sum = 1.19248e+06 --------------------------- iteration = : 8 grad.norm() = 333.796 pflug_sum = 1.31428e+06, max_pflug_sum = 1.31428e+06 --------------------------- iteration = : 9 grad.norm() = 307.313 pflug_sum = 1.41625e+06, max_pflug_sum = 1.41625e+06 --------------------------- iteration = : 10 grad.norm() = 262.334 pflug_sum = 1.49638e+06, max_pflug_sum = 1.49638e+06 --------------------------- Starting posterior sampling... Posterior sampling done. Average standard deviation of the posterior W: 0.182406672191487 Use ngme_post_samples() to access posterior samples and ngme_result() to access latent model parameters. Loading required package: Matrix This is rSPDE 2.6.0 - See https://davidbolin.github.io/rSPDE for vignettes and manuals. Attaching package: 'rSPDE' The following object is masked from 'package:ngme2': cross_validation Starting estimation... iteration = : 1 grad.norm() = 0.0978482 pflug_sum = 0, max_pflug_sum = 0 --------------------------- iteration = : 2 grad.norm() = 0.0616933 pflug_sum = 0.536835, max_pflug_sum = 0.536835 --------------------------- iteration = : 3 grad.norm() = 0.0993738 pflug_sum = 0.598393, max_pflug_sum = 0.598393 --------------------------- iteration = : 4 grad.norm() = 0.0197074 pflug_sum = 0.913024, max_pflug_sum = 0.913024 --------------------------- iteration = : 5 grad.norm() = 0.0113286 pflug_sum = 0.909865, max_pflug_sum = 0.913024 --------------------------- iteration = : 6 grad.norm() = 0.0728529 pflug_sum = 0.530169, max_pflug_sum = 0.913024 --------------------------- iteration = : 7 grad.norm() = 0.0562981 pflug_sum = 0.709158, max_pflug_sum = 0.913024 --------------------------- iteration = : 8 grad.norm() = 0.0228418 pflug_sum = 0.670477, max_pflug_sum = 0.913024 --------------------------- iteration = : 9 grad.norm() = 0.120301 pflug_sum = 0.807425, max_pflug_sum = 0.913024 --------------------------- iteration = : 10 grad.norm() = 0.136572 pflug_sum = -0.618443, max_pflug_sum = 0.913024 --------------------------- iteration = : 11 grad.norm() = 0.0596741 pflug_sum = -1.65303, max_pflug_sum = 0.913024 --------------------------- iteration = : 12 grad.norm() = 0.0480952 pflug_sum = -2.04819, max_pflug_sum = 0.913024 --------------------------- iteration = : 13 grad.norm() = 0.0751242 pflug_sum = -2.28146, max_pflug_sum = 0.913024 --------------------------- iteration = : 14 grad.norm() = 0.0133367 pflug_sum = -2.18568, max_pflug_sum = 0.913024 --------------------------- iteration = : 15 grad.norm() = 0.0134119 pflug_sum = -2.4969, max_pflug_sum = 0.913024 --------------------------- iteration = : 16 grad.norm() = 0.0356966 pflug_sum = -2.57351, max_pflug_sum = 0.913024 --------------------------- iteration = : 17 grad.norm() = 0.0146182 pflug_sum = -2.3927, max_pflug_sum = 0.913024 --------------------------- iteration = : 18 grad.norm() = 0.0626444 pflug_sum = -2.37174, max_pflug_sum = 0.913024 --------------------------- iteration = : 19 grad.norm() = 0.00976459 pflug_sum = -2.42595, max_pflug_sum = 0.913024 --------------------------- iteration = : 20 grad.norm() = 0.0364702 pflug_sum = -2.50787, max_pflug_sum = 0.913024 --------------------------- iteration = : 21 grad.norm() = 0.0359719 pflug_sum = -2.67576, max_pflug_sum = 0.913024 --------------------------- iteration = : 22 grad.norm() = 0.0159023 pflug_sum = -3.10104, max_pflug_sum = 0.913024 --------------------------- iteration = : 23 grad.norm() = 0.0751373 pflug_sum = -3.53313, max_pflug_sum = 0.913024 --------------------------- iteration = : 24 grad.norm() = 0.013733 pflug_sum = -3.69981, max_pflug_sum = 0.913024 --------------------------- iteration = : 25 grad.norm() = 0.0453626 pflug_sum = -3.89442, max_pflug_sum = 0.913024 --------------------------- iteration = : 26 grad.norm() = 0.0941321 pflug_sum = -3.70046, max_pflug_sum = 0.913024 --------------------------- iteration = : 27 grad.norm() = 0.122908 pflug_sum = -4.31389, max_pflug_sum = 0.913024 --------------------------- iteration = : 28 grad.norm() = 0.0290649 pflug_sum = -4.03683, max_pflug_sum = 0.913024 --------------------------- iteration = : 29 grad.norm() = 0.0362282 pflug_sum = -4.06691, max_pflug_sum = 0.913024 --------------------------- iteration = : 30 grad.norm() = 0.0269152 pflug_sum = -4.06646, max_pflug_sum = 0.913024 --------------------------- iteration = : 31 grad.norm() = 0.00874483 pflug_sum = -3.90435, max_pflug_sum = 0.913024 --------------------------- iteration = : 32 grad.norm() = 0.0614739 pflug_sum = -3.91586, max_pflug_sum = 0.913024 --------------------------- iteration = : 33 grad.norm() = 0.0329394 pflug_sum = -3.8428, max_pflug_sum = 0.913024 --------------------------- iteration = : 34 grad.norm() = 0.0757418 pflug_sum = -3.97057, max_pflug_sum = 0.913024 --------------------------- iteration = : 35 grad.norm() = 0.00797734 pflug_sum = -3.90412, max_pflug_sum = 0.913024 --------------------------- iteration = : 36 grad.norm() = 0.0769698 pflug_sum = -3.94222, max_pflug_sum = 0.913024 --------------------------- iteration = : 37 grad.norm() = 0.0290267 pflug_sum = -3.8621, max_pflug_sum = 0.913024 --------------------------- iteration = : 38 grad.norm() = 0.0166049 pflug_sum = -3.93832, max_pflug_sum = 0.913024 --------------------------- iteration = : 39 grad.norm() = 0.0306032 pflug_sum = -3.88065, max_pflug_sum = 0.913024 --------------------------- iteration = : 40 grad.norm() = 0.0522502 pflug_sum = -3.92611, max_pflug_sum = 0.913024 --------------------------- iteration = : 41 grad.norm() = 0.0292719 pflug_sum = -3.94087, max_pflug_sum = 0.913024 --------------------------- iteration = : 42 grad.norm() = 0.0107973 pflug_sum = -4.07192, max_pflug_sum = 0.913024 --------------------------- iteration = : 43 grad.norm() = 0.0345509 pflug_sum = -3.83396, max_pflug_sum = 0.913024 --------------------------- iteration = : 44 grad.norm() = 0.112398 pflug_sum = -4.15766, max_pflug_sum = 0.913024 --------------------------- iteration = : 45 grad.norm() = 0.0929521 pflug_sum = -4.69294, max_pflug_sum = 0.913024 --------------------------- iteration = : 46 grad.norm() = 0.0702741 pflug_sum = -5.0312, max_pflug_sum = 0.913024 --------------------------- iteration = : 47 grad.norm() = 0.0060716 pflug_sum = -5.09339, max_pflug_sum = 0.913024 --------------------------- iteration = : 48 grad.norm() = 0.038147 pflug_sum = -5.07442, max_pflug_sum = 0.913024 --------------------------- iteration = : 49 grad.norm() = 0.0409777 pflug_sum = -5.26237, max_pflug_sum = 0.913024 --------------------------- iteration = : 50 grad.norm() = 0.0146314 pflug_sum = -5.78897, max_pflug_sum = 0.913024 --------------------------- iteration = : 51 grad.norm() = 0.031141 pflug_sum = -5.48509, max_pflug_sum = 0.913024 --------------------------- iteration = : 52 grad.norm() = 0.0263634 pflug_sum = -5.71703, max_pflug_sum = 0.913024 --------------------------- iteration = : 53 grad.norm() = 0.00450449 pflug_sum = -5.59657, max_pflug_sum = 0.913024 --------------------------- iteration = : 54 grad.norm() = 0.0315191 pflug_sum = -5.68941, max_pflug_sum = 0.913024 --------------------------- iteration = : 55 grad.norm() = 0.0521376 pflug_sum = -5.38226, max_pflug_sum = 0.913024 --------------------------- iteration = : 56 grad.norm() = 0.0319413 pflug_sum = -5.88715, max_pflug_sum = 0.913024 --------------------------- iteration = : 57 grad.norm() = 0.0311783 pflug_sum = -7.02705, max_pflug_sum = 0.913024 --------------------------- iteration = : 58 grad.norm() = 0.0110639 pflug_sum = -7.61634, max_pflug_sum = 0.913024 --------------------------- iteration = : 59 grad.norm() = 0.0822262 pflug_sum = -7.8064, max_pflug_sum = 0.913024 --------------------------- iteration = : 60 grad.norm() = 0.030985 pflug_sum = -7.53767, max_pflug_sum = 0.913024 --------------------------- Pflug diagnostic satisfied: pflug_sum < 0.9 * max_pflug_sum for all chains. Starting posterior sampling... Posterior sampling done. Average standard deviation of the posterior W: 2.53725615429702 Use ngme_post_samples() to access posterior samples and ngme_result() to access latent model parameters. Saving _problems/test-core-fractional-model-81.R [1] 0.2288976 5 x 5 sparse Matrix of class "dgCMatrix" [1,] 0.8660254 . . . . [2,] -0.5000000 1.0 . . . [3,] . -0.5 1.0 . . [4,] . . -0.5 1.0 . [5,] . . . -0.5 1 [1] 0.2288976 [1] -0.1202982 [1] -0.1202982 [1] "rho" "c1" "c2" "rho (1st)" "rho (2nd)" "sigma_1" [7] "sigma_2" "sigma_1" Starting estimation... iteration = : 1 grad.norm() = 71.4007 pflug_sum = 0, max_pflug_sum = 0 --------------------------- iteration = : 2 grad.norm() = 68.3896 pflug_sum = 4883.06, max_pflug_sum = 4883.06 --------------------------- iteration = : 3 grad.norm() = 65.0619 pflug_sum = 9321.77, max_pflug_sum = 9321.77 --------------------------- iteration = : 4 grad.norm() = 61.4144 pflug_sum = 13310.7, max_pflug_sum = 13310.7 --------------------------- iteration = : 5 grad.norm() = 57.4176 pflug_sum = 16826.6, max_pflug_sum = 16826.6 --------------------------- iteration = : 6 grad.norm() = 53.0456 pflug_sum = 19871.7, max_pflug_sum = 19871.7 --------------------------- iteration = : 7 grad.norm() = 48.179 pflug_sum = 22425.8, max_pflug_sum = 22425.8 --------------------------- iteration = : 8 grad.norm() = 42.9026 pflug_sum = 24486.3, max_pflug_sum = 24486.3 --------------------------- iteration = : 9 grad.norm() = 37.363 pflug_sum = 26083.3, max_pflug_sum = 26083.3 --------------------------- iteration = : 10 grad.norm() = 31.3191 pflug_sum = 27253.1, max_pflug_sum = 27253.1 --------------------------- Starting posterior sampling... Posterior sampling done. Average standard deviation of the posterior W: NA Use ngme_post_samples() to access posterior samples and ngme_result() to access latent model parameters. [ FAIL 1 | WARN 0 | SKIP 9 | PASS 396 ] ══ Skipped tests (9) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test-compose-sum-ar1-matern.R:2:3', 'test-regression-fe-rank-check.R:25:3' • empty test (7): 'test-compose-bv.R:1:1', 'test-compose-bv.R:35:1', 'test-compose-bv.R:110:1', 'test-compose-bv.R:175:1', 'test-core-model-defs.R:20:1', 'test-core-model-defs.R:54:1', 'test-core-model-defs.R:77:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-core-fractional-model.R:77:3'): test fractional model ────────── Error in `path.expand(path)`: invalid 'path' argument Backtrace: ▆ 1. └─rSPDE::rspde.matern(mesh = mesh_2d, nu.upper.bound = 2, parameterization = "spde") at test-core-fractional-model.R:77:3 2. ├─base::do.call(...) 3. └─INLA (local) ``(...) 4. └─base::normalizePath(shlib) 5. └─base::path.expand(path) [ FAIL 1 | WARN 0 | SKIP 9 | PASS 396 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/Users/ripley/R/packages/tests-devel/ngme2.Rcheck/00check.log’ for details. 200.70 real 219.54 user 22.64 sys