Package evaluation to test SpatialOmicsGPs on Julia 1.14.0-DEV.1352 (749bc618c5*) started at 2025-12-09T23:52:26.325 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.79s ################################################################################ # Installation # Installing SpatialOmicsGPs... Resolving package versions... Installed CompositionsBase ──────────── v0.1.2 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed DiffResults ───────────────── v1.1.0 Installed InlineStrings ─────────────── v1.4.5 Installed FillArrays ────────────────── v1.15.0 Installed MacroTools ────────────────── v0.5.16 Installed ForwardDiff ───────────────── v1.3.0 Installed DataStructures ────────────── v0.19.3 Installed Adapt ─────────────────────── v4.4.0 Installed HypergeometricFunctions ───── v0.3.28 Installed ConstructionBase ──────────── v1.6.0 Installed AliasTables ───────────────── v1.1.3 Installed ArrayInterface ────────────── v7.22.0 Installed Functors ──────────────────── v0.5.2 Installed StatsBase ─────────────────── v0.34.9 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed Compat ────────────────────── v4.18.1 Installed OrderedCollections ────────── v1.8.1 Installed FaSTLMMlight ──────────────── v0.0.3 Installed TensorCore ────────────────── v0.1.1 Installed DataAPI ───────────────────── v1.16.0 Installed Optim ─────────────────────── v1.13.3 Installed Statistics ────────────────── v1.11.1 Installed DataValueInterfaces ───────── v1.0.0 Installed InvertedIndices ───────────── v1.3.1 Installed PositiveFactorizations ────── v0.2.4 Installed StatsAPI ──────────────────── v1.8.0 Installed SentinelArrays ────────────── v1.4.8 Installed CommonSubexpressions ──────── v0.3.1 Installed PrecompileTools ───────────── v1.3.3 Installed StaticArraysCore ──────────── v1.4.4 Installed IrrationalConstants ───────── v0.2.6 Installed Distances ─────────────────── v0.10.12 Installed NaNMath ───────────────────── v1.1.3 Installed Requires ──────────────────── v1.3.1 Installed StringManipulation ────────── v0.4.2 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed QuadGK ────────────────────── v2.11.2 Installed ChainRulesCore ────────────── v1.26.0 Installed DiffRules ─────────────────── v1.15.1 Installed LogExpFunctions ───────────── v0.3.29 Installed Rmath ─────────────────────── v0.9.0 Installed StatsFuns ─────────────────── v1.5.2 Installed FiniteDiff ────────────────── v2.29.0 Installed PrettyTables ──────────────── v3.1.2 Installed KernelFunctions ───────────── v0.10.66 Installed Distributions ─────────────── v0.25.122 Installed PtrArrays ─────────────────── v1.3.0 Installed EnumX ─────────────────────── v1.0.5 Installed Tables ────────────────────── v1.12.1 Installed NLSolversBase ─────────────── v7.10.0 Installed Reexport ──────────────────── v1.2.2 Installed Setfield ──────────────────── v1.1.2 Installed SpecialFunctions ──────────── v2.6.1 Installed Missings ──────────────────── v1.2.0 Installed PooledArrays ──────────────── v1.4.3 Installed JLLWrappers ───────────────── v1.7.1 Installed ZygoteRules ───────────────── v0.2.7 Installed TableTraits ───────────────── v1.0.1 Installed Preferences ───────────────── v1.5.0 Installed DataFrames ────────────────── v1.8.1 Installed LaTeXStrings ──────────────── v1.4.0 Installed Crayons ───────────────────── v4.1.1 Installed SortingAlgorithms ─────────── v1.2.2 Installed LineSearches ──────────────── v7.5.1 Installed PDMats ────────────────────── v0.11.36 Installed SpatialOmicsGPs ───────────── v0.0.3 Installed ADTypes ───────────────────── v1.20.0 Installed DocStringExtensions ───────── v0.9.5 Installed DifferentiationInterface ──── v0.7.12 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Updating `~/.julia/environments/v1.14/Project.toml` [e145bb07] + SpatialOmicsGPs v0.0.3 Updating `~/.julia/environments/v1.14/Manifest.toml` [47edcb42] + ADTypes v1.20.0 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [d360d2e6] + ChainRulesCore v1.26.0 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.12 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [4e289a0a] + EnumX v1.0.5 [26e330ee] + FaSTLMMlight v0.0.3 [1a297f60] + FillArrays v1.15.0 [6a86dc24] + FiniteDiff v2.29.0 [f6369f11] + ForwardDiff v1.3.0 [d9f16b24] + Functors v0.5.2 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [ec8451be] + KernelFunctions v0.10.66 [b964fa9f] + LaTeXStrings v1.4.0 [d3d80556] + LineSearches v7.5.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [d41bc354] + NLSolversBase v7.10.0 [77ba4419] + NaNMath v1.1.3 [429524aa] + Optim v1.13.3 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.36 [2dfb63ee] + PooledArrays v1.4.3 [85a6dd25] + PositiveFactorizations v0.2.4 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.2 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [a2af1166] + SortingAlgorithms v1.2.2 [e145bb07] + SpatialOmicsGPs v0.0.3 [276daf66] + SpecialFunctions v2.6.1 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.9 [4c63d2b9] + StatsFuns v1.5.2 [892a3eda] + StringManipulation v0.4.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [62fd8b95] + TensorCore v0.1.1 [700de1a5] + ZygoteRules v0.2.7 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 8.79s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 Precompilation failed after 12.76s ################################################################################ # Testing # Testing SpatialOmicsGPs Status `/tmp/jl_SCaMux/Project.toml` [a93c6f00] DataFrames v1.8.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.122 [26e330ee] FaSTLMMlight v0.0.3 [ec8451be] KernelFunctions v0.10.66 [429524aa] Optim v1.13.3 [e145bb07] SpatialOmicsGPs v0.0.3 [10745b16] Statistics v1.11.1 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_SCaMux/Manifest.toml` [47edcb42] ADTypes v1.20.0 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.22.0 [d360d2e6] ChainRulesCore v1.26.0 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.7.12 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.5 [26e330ee] FaSTLMMlight v0.0.3 [1a297f60] FillArrays v1.15.0 [6a86dc24] FiniteDiff v2.29.0 [f6369f11] ForwardDiff v1.3.0 [d9f16b24] Functors v0.5.2 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [ec8451be] KernelFunctions v0.10.66 [b964fa9f] LaTeXStrings v1.4.0 [d3d80556] LineSearches v7.5.1 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [d41bc354] NLSolversBase v7.10.0 [77ba4419] NaNMath v1.1.3 [429524aa] Optim v1.13.3 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.36 [2dfb63ee] PooledArrays v1.4.3 [85a6dd25] PositiveFactorizations v0.2.4 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.2 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [91c51154] SentinelArrays v1.4.8 [efcf1570] Setfield v1.1.2 [a2af1166] SortingAlgorithms v1.2.2 [e145bb07] SpatialOmicsGPs v0.0.3 [276daf66] SpecialFunctions v2.6.1 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.9 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [62fd8b95] TensorCore v0.1.1 [700de1a5] ZygoteRules v0.2.7 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [8e850b90] libblastrampoline_jll v5.15.0+0 Testing Running tests... Test Summary: | Total Time SpatialOmicsGPs.jl | 0 0.4s Testing SpatialOmicsGPs tests passed Testing completed after 321.86s PkgEval succeeded after 371.28s