Package evaluation of SBML on Julia 1.13.0-DEV.974 (7bbb213719*) started at 2025-08-12T13:24:01.614 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.97s ################################################################################ # Installation # Installing SBML... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [e5567a89] + SBML v1.6.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [ffbed154] + DocStringExtensions v0.9.5 [615f187c] + IfElse v0.1.1 [692b3bcd] + JLLWrappers v1.7.1 [21216c6a] + Preferences v1.5.0 [e5567a89] + SBML v1.6.0 [1986cc42] + Unitful v1.24.0 [94ce4f54] + Libiconv_jll v1.18.0+0 [bb12108a] + SBML_jll v5.20.1+0 ⌅ [02c8fc9c] + XML2_jll v2.13.6+1 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.13.0 [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 v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+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 To see why use `status --outdated -m` Installation completed after 4.57s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... ERROR: LoadError: The following 1 direct dependency failed to precompile: SymbolicsPreallocationToolsExt Failed to precompile SymbolicsPreallocationToolsExt [cf6f9317-8bac-542e-bce0-9dbc7ae7d397] to "/home/pkgeval/.julia/compiled/v1.13/SymbolicsPreallocationToolsExt/jl_bN4juO" (ProcessExited(1)). 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] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base ./module.jl:62 [2] _eval_using(to::Module, path::Expr) @ Base ./module.jl:137 [3] top-level scope @ ~/.julia/packages/Symbolics/qKoME/ext/SymbolicsPreallocationToolsExt.jl:5 [4] include(mod::Module, _path::String) @ Base ./Base.jl:311 [5] 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:3001 [6] top-level scope @ stdin:5 [7] eval(m::Module, e::Any) @ Core ./boot.jl:489 [8] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2847 [9] include_string @ ./loading.jl:2857 [inlined] [10] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [11] _start() @ Base ./client.jl:553 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:37 Precompilation failed after 463.64s ################################################################################ # Testing # Testing SBML Status `/tmp/jl_XQ9zXA/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 v1.24.0 [bb12108a] SBML_jll v5.20.1+0 [f43a241f] Downloads v1.7.0 [8f399da3] Libdl v1.11.0 [ea8e919c] SHA v0.7.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_XQ9zXA/Manifest.toml` [47edcb42] ADTypes v1.16.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.19.0 ⌅ [e2ed5e7c] Bijections v0.1.10 [d360d2e6] ChainRulesCore v1.26.0 [861a8166] Combinatorics v1.0.3 [38540f10] CommonSolve v0.2.4 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.0 [b152e2b5] CompositeTypes v0.1.4 [a33af91c] CompositionsBase v0.1.2 ⌅ [187b0558] ConstructionBase v1.5.6 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [5b8099bc] DomainSets v0.7.16 ⌅ [7c1d4256] DynamicPolynomials v0.5.7 [4e289a0a] EnumX v1.0.5 [e2ba6199] ExprTools v0.1.10 [55351af7] ExproniconLite v0.10.14 [1a297f60] FillArrays v1.13.0 [1fa38f19] Format v1.3.7 ⌅ [f6369f11] ForwardDiff v0.10.38 [069b7b12] FunctionWrappers v1.1.3 [77dc65aa] FunctionWrappersWrappers v0.1.3 [46192b85] GPUArraysCore v0.2.0 [34004b35] HypergeometricFunctions v0.3.28 [615f187c] IfElse v0.1.1 [8197267c] IntervalSets v0.7.11 [3587e190] InverseFunctions v0.1.17 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [ae98c720] Jieko v0.2.1 [b964fa9f] LaTeXStrings v1.4.0 [2ee39098] LabelledArrays v1.16.1 ⌅ [984bce1d] LambertW v0.4.6 [23fbe1c1] Latexify v0.16.9 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [2e0e35c7] Moshi v0.3.7 [102ac46a] MultivariatePolynomials v0.5.9 [d8a4904e] MutableArithmetics v1.6.4 [77ba4419] NaNMath v1.1.3 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [d236fae5] PreallocationTools v0.4.31 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v2.4.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [3cdcf5f2] RecipesBase v1.3.4 [731186ca] RecursiveArrayTools v3.37.0 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.8.0 [7e49a35a] RuntimeGeneratedFunctions v0.5.15 [e5567a89] SBML v1.6.0 [0bca4576] SciMLBase v2.108.0 [c0aeaf25] SciMLOperators v1.5.0 [53ae85a6] SciMLStructures v1.7.0 [efcf1570] Setfield v1.1.2 [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 [892a3eda] StringManipulation v0.4.1 [2efcf032] SymbolicIndexingInterface v0.3.42 ⌃ [19f23fe9] SymbolicLimits v0.2.1 ⌅ [d1185830] SymbolicUtils v2.1.3 ⌅ [0c5d862f] Symbolics v5.36.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 ⌅ [8ea1fca8] TermInterface v0.4.1 [a759f4b9] TimerOutputs v0.5.29 [1986cc42] Unitful v1.24.0 [a7c27f48] Unityper v0.1.6 [94ce4f54] Libiconv_jll v1.18.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [bb12108a] SBML_jll v5.20.1+0 ⌅ [02c8fc9c] XML2_jll v2.13.6+1 [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 v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [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 v1.13.0 [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+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. Testing Running tests... Precompiling packages... 3372.2 ms ✓ RecipesBase 1780.9 ms ✓ PreallocationTools 4737.6 ms ✓ SciMLOperators 1147.0 ms ✓ StaticArrays → StaticArraysChainRulesCoreExt 1167.8 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 4810.6 ms ✓ DomainSets 1434.4 ms ✓ Adapt → AdaptStaticArraysExt 1628.0 ms ✓ Accessors → StaticArraysExt 5321.7 ms ✓ SymbolicIndexingInterface 3739.1 ms ✓ StatsFuns → StatsFunsChainRulesCoreExt 1266.7 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 4124.8 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt 4186.2 ms ✓ Distributions → DistributionsChainRulesCoreExt 1410.3 ms ✓ IntervalSets → IntervalSetsRecipesBaseExt 1698.6 ms ✓ PreallocationTools → PreallocationToolsForwardDiffExt 1097.9 ms ✓ SciMLOperators → SciMLOperatorsStaticArraysCoreExt 1654.6 ms ✓ SciMLOperators → SciMLOperatorsSparseArraysExt 1613.2 ms ✓ DomainSets → DomainSetsRandomExt 5400.0 ms ✓ RecursiveArrayTools 3340.2 ms ✓ RecursiveArrayTools → RecursiveArrayToolsSparseArraysExt 2733.8 ms ✓ RecursiveArrayTools → RecursiveArrayToolsTablesExt 14598.4 ms ✓ RecursiveArrayTools → RecursiveArrayToolsForwardDiffExt 27246.4 ms ✓ SciMLBase 54179.5 ms ✓ LabelledArrays 3853.9 ms ✓ SciMLBase → SciMLBaseChainRulesCoreExt 146437.7 ms ✓ SymbolicUtils 9989.9 ms ✓ SymbolicLimits 229314.6 ms ✓ Symbolics ✗ Symbolics → SymbolicsPreallocationToolsExt 28 dependencies successfully precompiled in 560 seconds. 145 already precompiled. ERROR: LoadError: The following 1 direct dependency failed to precompile: SymbolicsPreallocationToolsExt Failed to precompile SymbolicsPreallocationToolsExt [cf6f9317-8bac-542e-bce0-9dbc7ae7d397] to "/home/pkgeval/.julia/compiled/v1.13/SymbolicsPreallocationToolsExt/jl_ZgkA5n" (ProcessExited(1)). 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] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base ./module.jl:62 [2] _eval_using(to::Module, path::Expr) @ Base ./module.jl:137 [3] top-level scope @ ~/.julia/packages/Symbolics/qKoME/ext/SymbolicsPreallocationToolsExt.jl:5 [4] include(mod::Module, _path::String) @ Base ./Base.jl:311 [5] 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:3001 [6] top-level scope @ stdin:5 [7] eval(m::Module, e::Any) @ Core ./boot.jl:489 [8] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2847 [9] include_string @ ./loading.jl:2857 [inlined] [10] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [11] _start() @ Base ./client.jl:553 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 568.82s ERROR: LoadError: Package SBML 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:311 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:320 [14] _start() @ Base ./client.jl:553 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1069.46s: package fails to precompile