Package evaluation of GaussianMarkovRandomFields on Julia 1.13.0-DEV.985 (9c94e7ae32*) started at 2025-08-15T02:32:00.413 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.57s ################################################################################ # Installation # Installing GaussianMarkovRandomFields... Resolving package versions... Installed Preconditioners ─ v0.6.1 Updating `~/.julia/environments/v1.13/Project.toml` [d5f06795] + GaussianMarkovRandomFields v0.3.1 Updating `~/.julia/environments/v1.13/Manifest.toml` [14f7f29c] + AMD v0.5.3 ⌅ [2169fc97] + AlgebraicMultigrid v0.5.1 [66dad0bd] + AliasTables v1.1.3 [fa961155] + CEnum v0.5.0 [944b1d66] + CodecZlib v0.7.8 [3da002f7] + ColorTypes v0.12.1 [38540f10] + CommonSolve v0.2.4 [bbf7d656] + CommonSubexpressions v0.3.1 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.0 [e2d170a0] + DataValueInterfaces v1.0.0 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [4e289a0a] + EnumX v1.0.5 [411431e0] + Extents v0.1.6 ⌅ [c061ca5d] + Ferrite v1.0.0 [4f95f4f8] + FerriteGmsh v1.2.1 [1a297f60] + FillArrays v1.13.0 [53c48c17] + FixedPointNumbers v0.8.5 ⌅ [f6369f11] + ForwardDiff v0.10.38 [d5f06795] + GaussianMarkovRandomFields v0.3.1 [68eda718] + GeoFormatTypes v0.4.4 ⌃ [cf35fbd7] + GeoInterface v1.4.1 [0edc0954] + GeoInterfaceMakie v0.1.9 [0329782f] + GeoInterfaceRecipes v1.0.2 ⌅ [5c1252a2] + GeometryBasics v0.4.11 [705231aa] + Gmsh v0.3.1 [34004b35] + HypergeometricFunctions v0.3.28 [8197267c] + IntervalSets v0.7.11 [92d709cd] + IrrationalConstants v0.2.4 [c8e1da08] + IterTools v1.10.0 [42fd0dbc] + IterativeSolvers v0.9.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 ⌃ [a90b1aa1] + LibGEOS v0.9.4 [9c8b4983] + LightXML v0.9.2 [f5a24dde] + LimitedLDLFactorizations v0.5.2 [7a12625a] + LinearMaps v3.11.4 [2ab3a3ac] + LogExpFunctions v0.3.29 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.16 ⌅ [20f20a25] + MakieCore v0.8.12 [e1d29d7a] + Missings v1.2.0 [77ba4419] + NaNMath v1.1.3 [b8a86587] + NearestNeighbors v0.4.22 [510215fc] + Observables v0.5.5 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [aea7be01] + PrecompileTools v1.3.2 [af69fa37] + Preconditioners v0.6.1 [21216c6a] + Preferences v1.5.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [fdea26ae] + SIMD v3.7.1 [043bf095] + SelectedInversion v0.1.5 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.5.1 [90137ffa] + StaticArrays v1.9.14 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.6 [4c63d2b9] + StatsFuns v1.5.0 ⌅ [09ab397b] + StructArrays v0.6.21 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [48a634ad] + Tensors v1.16.2 [3bb67fe8] + TranscodingStreams v0.11.3 [4004b06d] + VTKBase v1.0.1 [64499a7a] + WriteVTK v1.21.2 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.5+0 [5ae413db] + EarCut_jll v2.2.4+0 [2e619515] + Expat_jll v2.6.5+0 [4fce6fc7] + FLTK_jll v1.3.8+0 [a3f928ae] + Fontconfig_jll v2.16.0+0 [d7e528f0] + FreeType2_jll v2.13.4+0 [d604d12d] + GEOS_jll v3.13.1+1 [bd17208b] + GLU_jll v9.0.1+0 [b0724c58] + GettextRuntime_jll v0.22.4+0 [7746bdde] + Glib_jll v2.84.3+0 ⌅ [0234f1f7] + HDF5_jll v1.14.3+3 [e33a78d0] + Hwloc_jll v2.12.1+0 [aacddb02] + JpegTurbo_jll v3.1.1+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [dd4b983a] + LZO_jll v2.10.3+0 [e9f186c6] + Libffi_jll v3.4.7+0 [7e76a0d4] + Libglvnd_jll v1.7.1+1 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.41.0+0 [38a345b3] + Libuuid_jll v2.41.0+0 [18c40d15] + LinearElasticity_jll v5.0.0+0 [d00139f3] + METIS_jll v5.1.3+0 [86086c02] + MMG_jll v5.6.0+0 [7cb0a576] + MPICH_jll v4.3.1+0 [f1f71cc9] + MPItrampoline_jll v5.5.4+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [baad4e97] + OCCT_jll v7.7.2+0 ⌅ [fe0851c0] + OpenMPI_jll v4.1.8+1 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 ⌅ [30392449] + Pixman_jll v0.44.2+0 [f50d1b31] + Rmath_jll v0.5.1+0 ⌅ [a8d0f55d] + SCOTCH_jll v6.1.3+0 [02c8fc9c] + XML2_jll v2.14.4+0 [4f6342f7] + Xorg_libX11_jll 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[9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [781609d7] + GMP_jll v6.3.0+2 [deac9b47] + LibCURL_jll v8.15.0+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.7.15 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.2+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Building Preconditioners → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/a02fc23058e6264b0f73523e99e2dd1a20232dff/build.log` Installation completed after 12.93s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 279.54s ################################################################################ # Testing # Testing GaussianMarkovRandomFields Status `/tmp/jl_7idsOT/Project.toml` [14f7f29c] AMD v0.5.3 [4c88cf16] Aqua v0.8.14 [31c24e10] Distributions v0.25.120 ⌅ [c061ca5d] Ferrite v1.0.0 [4f95f4f8] FerriteGmsh v1.2.1 ⌅ [f6369f11] ForwardDiff v0.10.38 [d5f06795] GaussianMarkovRandomFields v0.3.1 ⌃ [cf35fbd7] GeoInterface v1.4.1 ⌅ [5c1252a2] GeometryBasics v0.4.11 [705231aa] Gmsh v0.3.1 [42fd0dbc] IterativeSolvers v0.9.4 [40e66cde] LDLFactorizations v0.10.1 ⌃ [a90b1aa1] LibGEOS v0.9.4 [7a12625a] LinearMaps v3.11.4 [af69fa37] Preconditioners v0.6.1 [e0db7c4e] ReTest v0.3.4 [043bf095] SelectedInversion v0.1.5 [276daf66] SpecialFunctions v2.5.1 [48a634ad] Tensors v1.16.2 ⌅ [e88e6eb3] Zygote v0.6.77 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_7idsOT/Manifest.toml` [14f7f29c] AMD 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SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Precompiling packages... 3921.2 ms ✓ StatsFuns → StatsFunsChainRulesCoreExt 1 dependency successfully precompiled in 5 seconds. 23 already precompiled. Precompiling packages... 5196.8 ms ✓ Distributions → DistributionsChainRulesCoreExt 1 dependency successfully precompiled in 8 seconds. 47 already precompiled. Precompiling packages... 1565.0 ms ✓ StaticArrays → StaticArraysChainRulesCoreExt 1 dependency successfully precompiled in 2 seconds. 12 already precompiled. Precompiling packages... 7234.1 ms ✓ KernelAbstractions 3076.4 ms ✓ KernelAbstractions → SparseArraysExt 2608.5 ms ✓ KernelAbstractions → LinearAlgebraExt 2787.8 ms ✓ StructArrays → StructArraysGPUArraysCoreExt 14989.6 ms ✓ GPUArrays 9982.1 ms ✓ Zygote → ZygoteDistancesExt 6 dependencies successfully precompiled in 42 seconds. 105 already precompiled. WARNING: Method definition _get_periodic_constraint(Any) in module GaussianMarkovRandomFieldsTests at /home/pkgeval/.julia/packages/GaussianMarkovRandomFields/D6R4D/test/spdes/test_matern.jl:7 overwritten at /home/pkgeval/.julia/packages/GaussianMarkovRandomFields/D6R4D/test/spatiotemporal/test_advection_diffusion.jl:8. WARNING: Method definition _get_dirichlet_constraint(Ferrite.Grid{1, C, T} where T<:Real where C<:(Ferrite.AbstractCell{refshape} where refshape<:(Ferrite.AbstractRefShape{refdim} where refdim)), Any, Any) in module GaussianMarkovRandomFieldsTests at /home/pkgeval/.julia/packages/GaussianMarkovRandomFields/D6R4D/test/spdes/test_matern.jl:22 overwritten at /home/pkgeval/.julia/packages/GaussianMarkovRandomFields/D6R4D/test/spatiotemporal/test_advection_diffusion.jl:23. Precompiling packages... 4596.4 ms ✓ OpenMPI_jll 7984.6 ms ✓ MakieCore 3476.9 ms ✓ GeoInterfaceMakie Info Given GaussianMarkovRandomFieldsLDLFactorizations was explicitly requested, output will be shown live  WARNING: Method definition linmap_cholesky_ldl_factorizations(AbstractArray{T, 2} where T) in module GaussianMarkovRandomFields at /home/pkgeval/.julia/packages/GaussianMarkovRandomFields/D6R4D/src/utils/linmap_cholesky.jl:37 overwritten in module GaussianMarkovRandomFieldsLDLFactorizations at /home/pkgeval/.julia/packages/GaussianMarkovRandomFields/D6R4D/ext/GaussianMarkovRandomFieldsLDLFactorizations.jl:17. ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. 11708.2 ms ? GaussianMarkovRandomFields → GaussianMarkovRandomFieldsLDLFactorizations 3 dependencies successfully precompiled in 31 seconds. 179 already precompiled. 1 dependencies failed but may be precompilable after restarting julia 1 dependency had output during precompilation: ┌ GaussianMarkovRandomFields → GaussianMarkovRandomFieldsLDLFactorizations │ [Output was shown above] └ WARNING: Method definition linmap_cholesky_ldl_factorizations(AbstractArray{T, 2} where T) in module GaussianMarkovRandomFields at /home/pkgeval/.julia/packages/GaussianMarkovRandomFields/D6R4D/src/utils/linmap_cholesky.jl:37 overwritten in module GaussianMarkovRandomFieldsLDLFactorizations at /home/pkgeval/.julia/packages/GaussianMarkovRandomFields/D6R4D/ext/GaussianMarkovRandomFieldsLDLFactorizations.jl:17. ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. WARNING: Method definition linmap_cholesky_ldl_factorizations(AbstractArray{T, 2} where T) in module GaussianMarkovRandomFields at /home/pkgeval/.julia/packages/GaussianMarkovRandomFields/D6R4D/src/utils/linmap_cholesky.jl:37 overwritten in module GaussianMarkovRandomFieldsLDLFactorizations at /home/pkgeval/.julia/packages/GaussianMarkovRandomFields/D6R4D/ext/GaussianMarkovRandomFieldsLDLFactorizations.jl:17. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(GaussianMarkovRandomFields.linmap_cholesky_ldl_factorizations), AbstractArray{T, 2} where T) in module GaussianMarkovRandomFields at /home/pkgeval/.julia/packages/GaussianMarkovRandomFields/D6R4D/src/utils/linmap_cholesky.jl:37 overwritten in module GaussianMarkovRandomFieldsLDLFactorizations at /home/pkgeval/.julia/packages/GaussianMarkovRandomFields/D6R4D/ext/GaussianMarkovRandomFieldsLDLFactorizations.jl:17. Pass Main.GaussianMarkovRandomFieldsTests: GMRF | 52 Linmap Cholesky | 6 AD Jacobian | 4 Zero map | 12 Outer product map | 9 Linear map with sqrt | 6 Cholesky Sqrt | 3 CholeskyFactorizedMap | 7 Symmetric block tridiagonal map | 18 SSM Bidiagonal map | 11 Full Cholesky Preconditioner | 7 Block Jacobi Preconditioner | 7 Tridiagonal block Gauss-Seidel preconditioners | 44 Test spatiotemporal preconditioner | 20 FEMDiscretization | 11 FEM Derivatives | 110 Info : Meshing 1D... 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Info : [ 0%] Meshing surface 1 (Plane, Frontal-Delaunay) Info : [ 60%] Meshing surface 2 (Plane, Frontal-Delaunay) Info : Done meshing 2D (Wall 0.610812s, CPU 0.610765s) Info : 11704 nodes 24965 elements Scattered mesh | 3 MaternSPDE | 100 RBMC Variance computations | 2 Pass Fail Total Gauss-Newton Optimizer | 5 1 6 Gauss-Newton Optimizer: Test Failed at /home/pkgeval/.julia/packages/GaussianMarkovRandomFields/D6R4D/test/optim/test_gauss_newton.jl:52 Expression: rel_err < 0.01 Evaluated: 0.15473726204110863 < 0.01 Main.GaussianMarkovRandomFieldsTests | 437 1 438 ERROR: LoadError: Some tests did not pass: 5 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/GaussianMarkovRandomFields/D6R4D/test/runtests.jl:4 Testing failed after 583.74s ERROR: LoadError: Package GaussianMarkovRandomFields errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2672 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2521 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:538 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:515 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:168 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:157 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [9] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:308 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:330 [14] _start() @ Base ./client.jl:563 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 910.29s: illegal method overwrites during precompilation