Package evaluation to test SBML on Julia 1.10.10 (c8be17dcfd*) started at 2026-02-02T15:43:18.295 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.10` Set-up completed after 5.39s ################################################################################ # Installation # Installing SBML... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [e5567a89] + SBML v1.6.0 Updating `~/.julia/environments/v1.10/Manifest.toml` [ffbed154] + DocStringExtensions v0.9.5 [615f187c] + IfElse v0.1.1 [692b3bcd] + JLLWrappers v1.7.1 [21216c6a] + Preferences v1.5.1 [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 [ade2ca70] + Dates [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [de0858da] + Printf [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [2f01184e] + SparseArrays v1.10.0 [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [4536629a] + OpenBLAS_jll v0.3.23+5 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+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 To see why use `status --outdated -m` Installation completed after 9.49s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 1911.4 ms ✓ LambertW 640.1 ms ✓ ConstructionBase 3848.4 ms ✓ MultivariatePolynomials 540.2 ms ✓ ConstructionBase → ConstructionBaseIntervalSetsExt 987.3 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 1506.6 ms ✓ Setfield 667.9 ms ✓ Unityper 1265.0 ms ✓ Unitful → ConstructionBaseUnitfulExt 2582.0 ms ✓ Accessors 599.2 ms ✓ ADTypes → ADTypesConstructionBaseExt 2792.6 ms ✓ DynamicPolynomials 1431.0 ms ✓ Accessors → LinearAlgebraExt 3547.2 ms ✓ SciMLOperators 1121.4 ms ✓ Accessors → TestExt 1540.3 ms ✓ Accessors → IntervalSetsExt 2041.5 ms ✓ Accessors → UnitfulExt 2702.5 ms ✓ SymbolicIndexingInterface 1431.2 ms ✓ Accessors → StaticArraysExt 850.7 ms ✓ SciMLOperators → SciMLOperatorsStaticArraysCoreExt 1392.0 ms ✓ SciMLOperators → SciMLOperatorsSparseArraysExt 5877.0 ms ✓ RecursiveArrayTools 12054.6 ms ✓ RecursiveArrayTools → RecursiveArrayToolsForwardDiffExt 1720.1 ms ✓ RecursiveArrayTools → RecursiveArrayToolsSparseArraysExt 24498.9 ms ✓ LabelledArrays 3616.3 ms ✓ RecursiveArrayTools → RecursiveArrayToolsStatisticsExt 47836.5 ms ✓ SymbolicUtils 26036.2 ms ✓ SciMLBase 5196.4 ms ✓ SymbolicLimits 3296.0 ms ✓ SciMLBase → SciMLBaseChainRulesCoreExt 45992.4 ms ✓ SciMLBase → SciMLBaseDistributionsExt 11582.9 ms ✓ SciMLBase → SciMLBaseForwardDiffExt 179109.8 ms ✓ Symbolics ✗ Symbolics → SymbolicsPreallocationToolsExt 32 dependencies successfully precompiled in 421 seconds. 127 already precompiled. ERROR: LoadError: The following 1 direct dependency failed to precompile: SymbolicsPreallocationToolsExt Failed to precompile SymbolicsPreallocationToolsExt [d479e226-fb54-5ebe-a75e-a7af7f39127f] to "/home/pkgeval/.julia/compiled/v1.10/SymbolicsPreallocationToolsExt/jl_AxZbiM". ERROR: LoadError: UndefVarError: `ForwardDiff` not defined Stacktrace: [1] include @ ./Base.jl:495 [inlined] [2] 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:2295 [3] top-level scope @ stdin:4 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 417.98s ################################################################################ # Testing # Testing SBML Status `/tmp/jl_oDoi4f/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 v1.6.0 [8f399da3] Libdl [ea8e919c] SHA v0.7.0 [2f01184e] SparseArrays v1.10.0 [8dfed614] Test Status `/tmp/jl_oDoi4f/Manifest.toml` [47edcb42] ADTypes v1.21.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.43 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.22.0 ⌅ [e2ed5e7c] Bijections v0.1.10 [d360d2e6] ChainRulesCore v1.26.0 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.6 [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 v1.15.1 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [5b8099bc] DomainSets v0.7.16 ⌅ [7c1d4256] DynamicPolynomials v0.5.7 [4e289a0a] EnumX v1.0.6 [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 [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 v0.7.13 [3587e190] InverseFunctions v0.1.17 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [ae98c720] Jieko v0.2.1 [b964fa9f] LaTeXStrings v1.4.0 [2ee39098] LabelledArrays v1.18.0 ⌅ [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 v0.3.7 ⌃ [102ac46a] MultivariatePolynomials v0.5.9 [d8a4904e] MutableArithmetics v1.6.7 [77ba4419] NaNMath v1.1.3 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 ⌃ [d236fae5] PreallocationTools v0.4.34 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.5.1 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [3cdcf5f2] RecipesBase v1.3.4 [731186ca] RecursiveArrayTools v3.47.0 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [7e49a35a] RuntimeGeneratedFunctions v0.5.17 [e5567a89] SBML v1.6.0 [0bca4576] SciMLBase v2.136.0 [a6db7da4] SciMLLogging v1.8.0 [c0aeaf25] SciMLOperators v1.15.1 [431bcebd] SciMLPublic v1.0.1 [53ae85a6] SciMLStructures v1.10.0 [efcf1570] Setfield v1.1.2 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [2efcf032] SymbolicIndexingInterface v0.3.46 ⌅ [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 [1986cc42] Unitful v1.28.0 [a7c27f48] Unityper v0.1.6 [61579ee1] Ghostscript_jll v9.55.1+0 [aacddb02] JpegTurbo_jll v3.1.4+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 v1.1.1 [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [8ba89e20] Distributed [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching [9fa8497b] Future [b77e0a4c] InteractiveUtils [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.10.0 [de0858da] Printf [3fa0cd96] REPL [9a3f8284] Random [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization [6462fe0b] Sockets [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.4.0+0 [e37daf67] LibGit2_jll v1.6.4+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.1010+0 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.23+5 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 [3f19e933] p7zip_jll v17.4.0+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... ERROR: LoadError: UndefVarError: `ForwardDiff` not defined Stacktrace: [1] include @ ./Base.jl:495 [inlined] [2] 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::String) @ Base ./loading.jl:2295 [3] top-level scope @ stdin:4 in expression starting at /home/pkgeval/.julia/packages/Symbolics/qKoME/ext/SymbolicsPreallocationToolsExt.jl:1 in expression starting at stdin:4 ┌ Error: Error during loading of extension SymbolicsPreallocationToolsExt of Symbolics, use `Base.retry_load_extensions()` to retry. │ exception = │ 1-element ExceptionStack: │ Failed to precompile SymbolicsPreallocationToolsExt [d479e226-fb54-5ebe-a75e-a7af7f39127f] to "/home/pkgeval/.julia/compiled/v1.10/SymbolicsPreallocationToolsExt/jl_CdHWvH". │ Stacktrace: │ [1] error(s::String) │ @ Base ./error.jl:35 │ [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) │ @ Base ./loading.jl:2542 │ [3] compilecache │ @ ./loading.jl:2414 [inlined] │ [4] (::Base.var"#971#972"{Base.PkgId})() │ @ Base ./loading.jl:2047 │ [5] mkpidlock(f::Base.var"#971#972"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool}) │ @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:93 │ [6] #mkpidlock#6 │ @ /opt/julia/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:88 [inlined] │ [7] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64}) │ @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:111 │ [8] #invokelatest#2 │ @ ./essentials.jl:894 [inlined] │ [9] invokelatest │ @ ./essentials.jl:889 [inlined] │ [10] maybe_cachefile_lock(f::Base.var"#971#972"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64) │ @ Base ./loading.jl:3057 │ [11] maybe_cachefile_lock │ @ ./loading.jl:3054 [inlined] │ [12] _require(pkg::Base.PkgId, env::Nothing) │ @ Base ./loading.jl:2043 │ [13] __require_prelocked(uuidkey::Base.PkgId, env::Nothing) │ @ Base ./loading.jl:1885 │ [14] #invoke_in_world#3 │ @ ./essentials.jl:926 [inlined] │ [15] invoke_in_world │ @ ./essentials.jl:923 [inlined] │ [16] _require_prelocked │ @ ./loading.jl:1876 [inlined] │ [17] _require_prelocked │ @ ./loading.jl:1875 [inlined] │ [18] run_extension_callbacks(extid::Base.ExtensionId) │ @ Base ./loading.jl:1368 │ [19] run_extension_callbacks(pkgid::Base.PkgId) │ @ Base ./loading.jl:1403 │ [20] run_package_callbacks(modkey::Base.PkgId) │ @ Base ./loading.jl:1227 │ [21] __require_prelocked(uuidkey::Base.PkgId, env::String) │ @ Base ./loading.jl:1892 │ [22] #invoke_in_world#3 │ @ ./essentials.jl:926 [inlined] │ [23] invoke_in_world │ @ ./essentials.jl:923 [inlined] │ [24] _require_prelocked(uuidkey::Base.PkgId, env::String) │ @ Base ./loading.jl:1876 │ [25] macro expansion │ @ ./loading.jl:1863 [inlined] │ [26] macro expansion │ @ ./lock.jl:270 [inlined] │ [27] __require(into::Module, mod::Symbol) │ @ Base ./loading.jl:1826 │ [28] #invoke_in_world#3 │ @ ./essentials.jl:926 [inlined] │ [29] invoke_in_world │ @ ./essentials.jl:923 [inlined] │ [30] require(into::Module, mod::Symbol) │ @ Base ./loading.jl:1819 │ [31] top-level scope │ @ ~/.julia/packages/SBML/mJIpc/test/runtests.jl:11 │ [32] include(fname::String) │ @ Base.MainInclude ./client.jl:487 │ [33] top-level scope │ @ none:6 │ [34] eval │ @ ./boot.jl:385 [inlined] │ [35] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:289 │ [36] _start() │ @ Base ./client.jl:550 └ @ Base loading.jl:1374 ┌ Warning: The downloaded model `/home/pkgeval/.julia/packages/SBML/mJIpc/test/data/00489-sbml-l3v2.xml' seems to be different from the expected one. Tests will likely fail. │ cksum = "2613c8e3fe67dc9226c6ed38acf5cc6dd3480d80ed9351c7c78ac97e981c860f" └ @ Main ~/.julia/packages/SBML/mJIpc/test/loadmodels.jl:186 ┌ Warning: The downloaded model `/home/pkgeval/.julia/packages/SBML/mJIpc/test/data/00489-sbml-l3v2.xml' seems to be different from the expected one. Tests will likely fail. │ cksum = "2613c8e3fe67dc9226c6ed38acf5cc6dd3480d80ed9351c7c78ac97e981c860f" └ @ Main ~/.julia/packages/SBML/mJIpc/test/loadmodels.jl:186 Test Summary: | Pass Broken Total Time SBML test suite | 454 1 455 1m48.6s Testing SBML tests passed Testing completed after 322.37s PkgEval succeeded after 784.03s