Package evaluation to test SBML on Julia 1.12.7-DEV.42 (6f510b6086*) started at 2026-06-19T12:46:36.810 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 8.35s ################################################################################ # Installation # Installing SBML... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [e5567a89] + SBML v1.6.0 Updating `~/.julia/environments/v1.12/Manifest.toml` [ffbed154] + DocStringExtensions v0.9.5 [615f187c] + IfElse v0.1.1 [692b3bcd] + JLLWrappers v1.8.0 [21216c6a] + Preferences v1.5.2 [e5567a89] + SBML v1.6.0 [1986cc42] + Unitful v1.28.0 [94ce4f54] + Libiconv_jll v1.18.0+0 [bb12108a] + SBML_jll v5.21.0+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.12.0 [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 6.19s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 5683.4 ms ✓ LambertW 3985.3 ms ✓ ConstructionBase 7870.6 ms ✓ DynamicPolynomials 1258.2 ms ✓ PreallocationTools → PreallocationToolsForwardDiffExt 4090.1 ms ✓ Unityper 847.3 ms ✓ ConstructionBase → ConstructionBaseIntervalSetsExt 1479.0 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 800.4 ms ✓ ADTypes → ADTypesConstructionBaseExt 3123.7 ms ✓ Setfield 8327.0 ms ✓ Accessors 2098.3 ms ✓ Unitful → ConstructionBaseUnitfulExt 2214.7 ms ✓ Accessors → LinearAlgebraExt 1827.9 ms ✓ Accessors → TestExt 2281.1 ms ✓ Accessors → IntervalSetsExt 2165.2 ms ✓ Accessors → UnitfulExt 1598.1 ms ✓ Accessors → StaticArraysExt 7734.8 ms ✓ SciMLOperators 6292.2 ms ✓ SymbolicIndexingInterface 1078.2 ms ✓ SciMLOperators → SciMLOperatorsStaticArraysCoreExt 1839.7 ms ✓ SciMLOperators → SciMLOperatorsSparseArraysExt 13088.3 ms ✓ RecursiveArrayTools 1380.4 ms ✓ RecursiveArrayTools → RecursiveArrayToolsStatisticsExt 2030.4 ms ✓ RecursiveArrayTools → RecursiveArrayToolsSparseArraysExt 1893.0 ms ✓ RecursiveArrayTools → RecursiveArrayToolsForwardDiffExt 41850.3 ms ✓ SciMLBase 49926.8 ms ✓ LabelledArrays 69701.3 ms ✓ SciMLBase → SciMLBaseDistributionsExt 4406.6 ms ✓ SciMLBase → SciMLBaseChainRulesCoreExt 31779.1 ms ✓ SciMLBase → SciMLBaseForwardDiffExt 123377.9 ms ✓ SymbolicUtils 12588.5 ms ✓ SymbolicLimits 168637.8 ms ✓ Symbolics ✗ Symbolics → SymbolicsPreallocationToolsExt 32 dependencies successfully precompiled in 610 seconds. 157 already precompiled. 24 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 95 dependents of these packages may trigger further precompilation to work with the unexpected versions. ERROR: LoadError: The following 1 direct dependency failed to precompile: Symbolics → SymbolicsPreallocationToolsExt Failed to precompile SymbolicsPreallocationToolsExt [d479e226-fb54-5ebe-a75e-a7af7f39127f] to "/home/pkgeval/.julia/compiled/v1.12/SymbolicsPreallocationToolsExt/jl_RvVuD9". ERROR: LoadError: UndefVarError: `ForwardDiff` not defined in `PreallocationTools` Suggestion: check for spelling errors or missing imports. Hint: ForwardDiff is loaded but not imported in the active module Main. Stacktrace: [1] top-level scope @ ~/.julia/packages/Symbolics/qKoME/ext/SymbolicsPreallocationToolsExt.jl:5 [2] include(mod::Module, _path::String) @ Base ./Base.jl:306 [3] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base ./loading.jl:3027 [4] top-level scope @ stdin:5 [5] eval(m::Module, e::Any) @ Core ./boot.jl:489 [6] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2873 [7] include_string @ ./loading.jl:2883 [inlined] [8] exec_options(opts::Base.JLOptions) @ Base ./client.jl:315 [9] _start() @ Base ./client.jl:550 in expression starting at /home/pkgeval/.julia/packages/Symbolics/qKoME/ext/SymbolicsPreallocationToolsExt.jl:1 in expression starting at stdin: in expression starting at /PkgEval.jl/scripts/precompile.jl:34 Precompilation failed after 623.14s ################################################################################ # Testing # Testing SBML Status `/tmp/jl_0kIepK/Project.toml` ⌅ [187b0558] ConstructionBase v1.5.6 [ffbed154] DocStringExtensions v0.9.5 [615f187c] IfElse v0.1.1 [e5567a89] SBML v1.6.0 ⌅ [0c5d862f] Symbolics v5.36.0 [1986cc42] Unitful v1.28.0 [bb12108a] SBML_jll v5.21.0+0 [f43a241f] Downloads v1.7.0 [8f399da3] Libdl v1.11.0 [ea8e919c] SHA v0.7.0 [2f01184e] SparseArrays v1.12.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_0kIepK/Manifest.toml` [47edcb42] ADTypes v1.22.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.44 [79e6a3ab] Adapt v4.6.1 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.25.0 ⌅ [e2ed5e7c] Bijections v0.1.10 [d360d2e6] ChainRulesCore v1.26.1 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.7 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.1 [b152e2b5] CompositeTypes v0.1.4 [a33af91c] CompositionsBase v0.1.2 ⌅ [187b0558] ConstructionBase v1.5.6 [9a962f9c] DataAPI v1.16.0 ⌅ [864edb3b] DataStructures v0.18.22 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.16.0 [31c24e10] Distributions v0.25.127 [ffbed154] DocStringExtensions v0.9.5 ⌅ [5b8099bc] DomainSets v0.7.18 ⌅ [7c1d4256] DynamicPolynomials v0.5.7 [4e289a0a] EnumX v1.0.7 [e2ba6199] ExprTools v0.1.10 [55351af7] ExproniconLite v0.10.14 [1a297f60] FillArrays v1.16.0 [1fa38f19] Format v1.3.7 ⌅ [f6369f11] ForwardDiff v0.10.39 [a85aefff] FunctionMaps v0.1.2 [069b7b12] FunctionWrappers v1.1.3 [77dc65aa] FunctionWrappersWrappers v1.9.1 [46192b85] GPUArraysCore v0.2.0 [34004b35] HypergeometricFunctions v0.3.28 [615f187c] IfElse v0.1.1 [8197267c] IntervalSets v0.7.14 [3587e190] InverseFunctions v0.1.17 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [ae98c720] Jieko v0.2.1 [b964fa9f] LaTeXStrings v1.4.0 [2ee39098] LabelledArrays v1.19.0 ⌅ [984bce1d] LambertW v0.4.6 [23fbe1c1] Latexify v0.16.10 ⌅ [2ab3a3ac] LogExpFunctions v0.3.29 [e6f89c97] LoggingExtras v1.2.0 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [2e0e35c7] Moshi v0.3.8 ⌃ [102ac46a] MultivariatePolynomials v0.5.9 [d8a4904e] MutableArithmetics v1.8.0 [77ba4419] NaNMath v1.1.4 ⌅ [bac558e1] OrderedCollections v1.8.2 [90014a1f] PDMats v0.11.37 ⌃ [d236fae5] PreallocationTools v0.4.34 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.3 [3cdcf5f2] RecipesBase v1.3.4 ⌅ [731186ca] RecursiveArrayTools v3.54.0 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [7e49a35a] RuntimeGeneratedFunctions v0.5.19 [e5567a89] SBML v1.6.0 ⌅ [0bca4576] SciMLBase v2.155.1 ⌅ [a6db7da4] SciMLLogging v1.10.1 [c0aeaf25] SciMLOperators v1.22.0 [431bcebd] SciMLPublic v1.0.1 [53ae85a6] SciMLStructures v1.10.0 [efcf1570] Setfield v1.1.2 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.8.0 [90137ffa] StaticArrays v1.9.18 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.12 [4c63d2b9] StatsFuns v2.2.0 [2efcf032] SymbolicIndexingInterface v0.3.48 ⌅ [19f23fe9] SymbolicLimits v0.2.1 ⌅ [d1185830] SymbolicUtils v2.1.3 ⌅ [0c5d862f] Symbolics v5.36.0 ⌅ [8ea1fca8] TermInterface v0.4.1 [a759f4b9] TimerOutputs v0.5.29 [781d530d] TruncatedStacktraces v1.4.0 [1986cc42] Unitful v1.28.0 [a7c27f48] Unityper v0.1.6 [61579ee1] Ghostscript_jll v9.55.1+0 [aacddb02] JpegTurbo_jll v3.1.5+0 [94ce4f54] Libiconv_jll v1.18.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [bb12108a] SBML_jll v5.21.0+0 ⌅ [02c8fc9c] XML2_jll v2.13.9+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.1 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.15.0+0 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.6+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.7.0+0 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... 12314.8 ms ✓ RecursiveArrayTools 6314.6 ms ✓ SpecialFunctions 1523.2 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 1693.8 ms ✓ Accessors → StaticArraysExt 7083.4 ms ✓ DomainSets 1411.7 ms ✓ RecursiveArrayTools → RecursiveArrayToolsStatisticsExt 2114.1 ms ✓ RecursiveArrayTools → RecursiveArrayToolsSparseArraysExt 4820.6 ms ✓ SpecialFunctions → SpecialFunctionsChainRulesCoreExt 2574.4 ms ✓ HypergeometricFunctions 13623.5 ms ✓ ForwardDiff 1468.5 ms ✓ DomainSets → DomainSetsRandomExt 42245.7 ms ✓ SciMLBase 5534.2 ms ✓ StatsFuns 3733.1 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt 982.1 ms ✓ PreallocationTools → PreallocationToolsForwardDiffExt 2952.3 ms ✓ RecursiveArrayTools → RecursiveArrayToolsForwardDiffExt 4176.1 ms ✓ SciMLBase → SciMLBaseChainRulesCoreExt 10369.7 ms ✓ SciMLBase → SciMLBaseForwardDiffExt 1162.7 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 4121.6 ms ✓ StatsFuns → StatsFunsChainRulesCoreExt 10938.5 ms ✓ Distributions 10197.1 ms ✓ LabelledArrays 3926.3 ms ✓ Distributions → DistributionsTestExt 7580.5 ms ✓ Distributions → DistributionsChainRulesCoreExt 5210.3 ms ✓ SciMLBase → SciMLBaseDistributionsExt 49587.9 ms ✓ SymbolicUtils 12562.9 ms ✓ SymbolicLimits 50805.9 ms ✓ Symbolics ✗ Symbolics → SymbolicsPreallocationToolsExt 28 dependencies successfully precompiled in 298 seconds. 149 already precompiled. 27 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, DocStringExtensions, Downloads, IfElse, InteractiveUtils, JLLWrappers, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Preferences, Printf, Serialization, SparseArrays, StyledStrings, SuiteSparse_jll, TOML, Test, Zlib_jll and nghttp2_jll). Restart julia to access the new versions. Otherwise, 93 dependents of these packages may trigger further precompilation to work with the unexpected versions. ERROR: LoadError: The following 1 direct dependency failed to precompile: Symbolics → SymbolicsPreallocationToolsExt Failed to precompile SymbolicsPreallocationToolsExt [d479e226-fb54-5ebe-a75e-a7af7f39127f] to "/home/pkgeval/.julia/compiled/v1.12/SymbolicsPreallocationToolsExt/jl_At18xV". ERROR: LoadError: UndefVarError: `ForwardDiff` not defined in `PreallocationTools` Suggestion: check for spelling errors or missing imports. Hint: ForwardDiff is loaded but not imported in the active module Main. Stacktrace: [1] top-level scope @ ~/.julia/packages/Symbolics/qKoME/ext/SymbolicsPreallocationToolsExt.jl:5 [2] include(mod::Module, _path::String) @ Base ./Base.jl:306 [3] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base ./loading.jl:3027 [4] top-level scope @ stdin:5 [5] eval(m::Module, e::Any) @ Core ./boot.jl:489 [6] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2873 [7] include_string @ ./loading.jl:2883 [inlined] [8] exec_options(opts::Base.JLOptions) @ Base ./client.jl:315 [9] _start() @ Base ./client.jl:550 in expression starting at /home/pkgeval/.julia/packages/Symbolics/qKoME/ext/SymbolicsPreallocationToolsExt.jl:1 in expression starting at stdin: in expression starting at /home/pkgeval/.julia/packages/SBML/mJIpc/test/runtests.jl:10 Testing failed after 314.14s ERROR: LoadError: Package SBML errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/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/v1.12/Pkg/src/Operations.jl:2538 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2387 [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/v1.12/Pkg/src/API.jl:552 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:169 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:156 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:306 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:317 [12] _start() @ Base ./client.jl:550 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 982.84s: package fails to precompile