Package evaluation to test SBML on Julia 1.14.0-DEV.1918 (78a0dc1151*) started at 2026-03-19T15:20:27.498 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.28s ################################################################################ # Installation # Installing SBML... Resolving package versions... Installed SBML_jll ──────────── v5.21.0+0 Installed Libiconv_jll ──────── v1.18.0+0 Installed IfElse ────────────── v0.1.1 Installed JLLWrappers ───────── v1.7.1 Installed SBML ──────────────── v1.6.0 Installed DocStringExtensions ─ v0.9.5 Installed Unitful ───────────── v1.28.0 Installed Preferences ───────── v1.5.2 Installed XML2_jll ──────────── v2.13.9+0 Installing 3 artifacts Installed artifact Libiconv 1.9 MiB Installed artifact XML2 2.5 MiB Installed artifact SBML 6.0 MiB Updating `~/.julia/environments/v1.14/Project.toml` [e5567a89] + SBML v1.6.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [ffbed154] + DocStringExtensions v0.9.5 [615f187c] + IfElse v0.1.1 [692b3bcd] + JLLWrappers v1.7.1 [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 v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [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 v0.3.30+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [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 To see why use `status --outdated -m` Installation completed after 9.41s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 6278.1 ms ✓ TestEnv 1 dependency successfully precompiled in 6 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling packages... 10409.4 ms ✓ MacroTools 885.3 ms ✓ Reexport 1927.5 ms ✓ ConstructionBase 3982.4 ms ✓ IrrationalConstants 1188.0 ms ✓ StatsAPI 3438.5 ms ✓ Format 1544.0 ms ✓ IntervalSets 3179.1 ms ✓ Combinatorics 1292.2 ms ✓ TermInterface 1201.3 ms ✓ CommonSolve 1168.3 ms ✓ LaTeXStrings 1662.4 ms ✓ Statistics 1790.8 ms ✓ StaticArraysCore 1778.1 ms ✓ CompositeTypes 2101.4 ms ✓ IfElse 2127.8 ms ✓ PtrArrays 1906.8 ms ✓ DataAPI 1552.6 ms ✓ SciMLPublic 6075.2 ms ✓ ExproniconLite 1351.9 ms ✓ CommonWorldInvalidations 1112.3 ms ✓ InverseFunctions 979.4 ms ✓ CompositionsBase 2057.2 ms ✓ AbstractTrees 1382.8 ms ✓ EnumX 1317.7 ms ✓ Bijections 3624.9 ms ✓ FillArrays 2136.2 ms ✓ LambertW 1320.0 ms ✓ ExprTools 2409.2 ms ✓ OrderedCollections 2023.2 ms ✓ FunctionWrappers 2515.1 ms ✓ ADTypes 2476.9 ms ✓ DocStringExtensions 1868.2 ms ✓ IteratorInterfaceExtensions 1583.1 ms ✓ NaNMath 1965.3 ms ✓ Requires 4433.7 ms ✓ PDMats 63972.8 ms ✓ Unitful 1989.3 ms ✓ LoggingExtras 2104.5 ms ✓ Compat 2007.2 ms ✓ Preferences 24122.1 ms ✓ MutableArithmetics 3341.7 ms ✓ CommonSubexpressions 2252.8 ms ✓ Unityper 1170.0 ms ✓ IntervalSets → IntervalSetsRandomExt 1412.2 ms ✓ ConstructionBase → ConstructionBaseIntervalSetsExt 2953.7 ms ✓ Statistics → SparseArraysExt 1291.1 ms ✓ IntervalSets → IntervalSetsStatisticsExt 1349.5 ms ✓ DiffResults 5850.3 ms ✓ Setfield 1991.4 ms ✓ AliasTables 1305.3 ms ✓ Missings 6997.3 ms ✓ Jieko 2679.9 ms ✓ InverseFunctions → InverseFunctionsDatesExt 2883.3 ms ✓ InverseFunctions → InverseFunctionsTestExt 1168.8 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 2732.5 ms ✓ FillArrays → FillArraysSparseArraysExt 2124.9 ms ✓ FillArrays → FillArraysStatisticsExt 5506.5 ms ✓ TimerOutputs 1432.7 ms ✓ RuntimeGeneratedFunctions 1607.9 ms ✓ FunctionWrappersWrappers 1655.8 ms ✓ ADTypes → ADTypesConstructionBaseExt 3213.9 ms ✓ LogExpFunctions 2437.6 ms ✓ Adapt 2934.7 ms ✓ FillArrays → FillArraysPDMatsExt 4620.4 ms ✓ Unitful → ConstructionBaseUnitfulExt 4833.1 ms ✓ Unitful → PrintfExt 4545.4 ms ✓ Unitful → InverseFunctionsUnitfulExt 3869.8 ms ✓ Unitful → NaNMathExt 1546.2 ms ✓ Compat → CompatLinearAlgebraExt 3554.2 ms ✓ PrecompileTools 2722.8 ms ✓ JLLWrappers 2664.0 ms ✓ SciMLLogging 31196.3 ms ✓ Moshi 9207.6 ms ✓ Accessors 1135.8 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1928.5 ms ✓ ArrayInterface 1689.9 ms ✓ Adapt → AdaptSparseArraysExt 2330.6 ms ✓ GPUArraysCore 5448.1 ms ✓ ChainRulesCore 7689.6 ms ✓ DataStructures 25571.2 ms ✓ StaticArrays 6726.0 ms ✓ RecipesBase 4365.0 ms ✓ Rmath_jll 4771.6 ms ✓ OpenSpecFun_jll 5042.4 ms ✓ Libiconv_jll 3710.4 ms ✓ JpegTurbo_jll 2662.2 ms ✓ Accessors → TestExt 5309.2 ms ✓ Accessors → IntervalSetsExt 6961.3 ms ✓ Accessors → LinearAlgebraExt 5358.4 ms ✓ Accessors → UnitfulExt 1622.4 ms ✓ ArrayInterface → ArrayInterfaceStaticArraysCoreExt 3067.8 ms ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 3922.0 ms ✓ SciMLStructures 3737.7 ms ✓ PreallocationTools 1049.0 ms ✓ ArrayInterface → ArrayInterfaceGPUArraysCoreExt 2191.8 ms ✓ ChainRulesCore → ChainRulesCoreSparseArraysExt 1679.0 ms ✓ ADTypes → ADTypesChainRulesCoreExt 8085.3 ms ✓ LogExpFunctions → LogExpFunctionsChainRulesCoreExt 1317.4 ms ✓ ArrayInterface → ArrayInterfaceChainRulesCoreExt 3563.6 ms ✓ SortingAlgorithms 3969.9 ms ✓ QuadGK 4500.9 ms ✓ StaticArrays → StaticArraysStatisticsExt 4402.8 ms ✓ StaticArrays → StaticArraysChainRulesCoreExt 4119.3 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 11147.1 ms ✓ DomainSets 6296.2 ms ✓ FillArrays → FillArraysStaticArraysExt 3600.3 ms ✓ Adapt → AdaptStaticArraysExt 4077.9 ms ✓ Accessors → StaticArraysExt 3125.7 ms ✓ IntervalSets → IntervalSetsRecipesBaseExt 3456.0 ms ✓ Rmath 8230.9 ms ✓ SpecialFunctions 3466.6 ms ✓ XML2_jll 3821.0 ms ✓ Ghostscript_jll 9164.0 ms ✓ SciMLOperators 8209.5 ms ✓ SymbolicIndexingInterface 13057.1 ms ✓ MultivariatePolynomials 11484.3 ms ✓ StatsBase 4658.4 ms ✓ DomainSets → DomainSetsRandomExt 9574.3 ms ✓ SpecialFunctions → SpecialFunctionsChainRulesCoreExt 4897.9 ms ✓ HypergeometricFunctions 1796.6 ms ✓ DiffRules 3070.0 ms ✓ SBML_jll 11133.6 ms ✓ Latexify 1839.6 ms ✓ SciMLOperators → SciMLOperatorsStaticArraysCoreExt 3527.2 ms ✓ SciMLOperators → SciMLOperatorsSparseArraysExt 14471.3 ms ✓ RecursiveArrayTools 7324.6 ms ✓ DynamicPolynomials 3199.0 ms ✓ PDMats → StatsBaseExt 5363.6 ms ✓ StatsFuns 12369.9 ms ✓ ForwardDiff 36403.9 ms ✓ SBML 7674.6 ms ✓ Latexify → SparseArraysExt 6051.9 ms ✓ Unitful → LatexifyExt 3874.2 ms ✓ RecursiveArrayTools → RecursiveArrayToolsSparseArraysExt 4093.5 ms ✓ RecursiveArrayTools → RecursiveArrayToolsStatisticsExt 9201.0 ms ✓ StatsFuns → StatsFunsChainRulesCoreExt 3182.0 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 14109.7 ms ✓ Distributions 4214.0 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt 5452.4 ms ✓ Unitful → ForwardDiffExt 3111.1 ms ✓ PreallocationTools → PreallocationToolsForwardDiffExt 4244.9 ms ✓ RecursiveArrayTools → RecursiveArrayToolsForwardDiffExt 54159.2 ms ✓ SciMLBase 5526.9 ms ✓ Distributions → DistributionsTestExt 5256.7 ms ✓ Distributions → DistributionsChainRulesCoreExt 10016.5 ms ✓ LabelledArrays 6924.0 ms ✓ SciMLBase → SciMLBaseChainRulesCoreExt 7760.8 ms ✓ SciMLBase → SciMLBaseForwardDiffExt 7720.9 ms ✓ SciMLBase → SciMLBaseDistributionsExt 57580.7 ms ✓ SymbolicUtils 12513.0 ms ✓ SymbolicLimits 82684.3 ms ✓ Symbolics 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  @ ./module.jl:137 [inlined]  [3] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137  [4] top-level scope  @ ~/.julia/packages/Symbolics/qKoME/ext/SymbolicsPreallocationToolsExt.jl:5  [5] include(mod::Module, _path::String)  @ Base ./Base.jl:323  [6] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3289  [7] top-level scope  @ stdin:5  [8] eval(m::Module, e::Any)  @ Core ./boot.jl:517  [9] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3131  [10] include_string  @ ./loading.jl:3141 [inlined]  [11] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [12] _start()  @ Base ./client.jl:585 in expression starting at /home/pkgeval/.julia/packages/Symbolics/qKoME/ext/SymbolicsPreallocationToolsExt.jl:1 in expression starting at stdin:5 ✗ Symbolics → SymbolicsPreallocationToolsExt 152 dependencies successfully precompiled in 994 seconds. 36 already precompiled. Precompilation completed after 643.28s ################################################################################ # Testing # Testing SBML Status `/tmp/jl_fqDubQ/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 v1.0.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_fqDubQ/Manifest.toml` [47edcb42] ADTypes v1.21.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.43 [79e6a3ab] Adapt v4.5.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.23.0 ⌅ [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 v1.0.7 [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 [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 v1.3.3 [21216c6a] Preferences v1.5.2 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.2 [3cdcf5f2] RecipesBase v1.3.4 [731186ca] RecursiveArrayTools v3.48.0 [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 v2.150.0 [a6db7da4] SciMLLogging v1.9.1 [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 v2.7.1 [90137ffa] StaticArrays v1.9.18 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [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 v1.1.2 [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 v1.13.0 [b27032c2] LibCURL v1.0.0 [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 v1.14.0 [de0858da] Printf 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 [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 v8.19.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.30+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.5+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.8.0+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... 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  @ ./module.jl:137 [inlined]  [3] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137  [4] top-level scope  @ ~/.julia/packages/Symbolics/qKoME/ext/SymbolicsPreallocationToolsExt.jl:5  [5] include(mod::Module, _path::String)  @ Base ./Base.jl:323  [6] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3289  [7] top-level scope  @ stdin:5  [8] eval(m::Module, e::Any)  @ Core ./boot.jl:517  [9] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3131  [10] include_string  @ ./loading.jl:3141 [inlined]  [11] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [12] _start()  @ Base ./client.jl:585 in expression starting at /home/pkgeval/.julia/packages/Symbolics/qKoME/ext/SymbolicsPreallocationToolsExt.jl:1 in expression starting at stdin:5 1 dependency had output during precompilation: ┌ Symbolics → SymbolicsPreallocationToolsExt │ [Output was shown above] └ ┌ Error: Error during loading of extension SymbolicsPreallocationToolsExt of Symbolics, use `Base.retry_load_extensions()` to retry. │ exception = │ 1-element ExceptionStack: │ The following 1 package failed to precompile: │ │ Symbolics → SymbolicsPreallocationToolsExt │ Failed to precompile SymbolicsPreallocationToolsExt [cf6f9317-8bac-542e-bce0-9dbc7ae7d397] to "/home/pkgeval/.julia/compiled/v1.14/SymbolicsPreallocationToolsExt/jl_xPUZ5B" (ProcessExited(1)). │ └ @ Base loading.jl:1776 SBML flux model loading: Test Failed at /home/pkgeval/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:46 Expression: mets[10:12] == ["M_akg_e", "M_fum_c", "M_pyr_c"] Evaluated: ["M_xu5p_D_c", "M_h2o_b", "M_amp_c"] == ["M_akg_e", "M_fum_c", "M_pyr_c"] Stacktrace: [1] top-level scope @ ~/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:17 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [3] macro expansion @ ~/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:46 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined] SBML flux model loading: Test Failed at /home/pkgeval/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:47 Expression: rxns[10:12] == ["R_H2Ot", "R_PGL", "R_EX_glc_e_"] Evaluated: ["R_FBA", "R_FORt", "R_EX_for_e_"] == ["R_H2Ot", "R_PGL", "R_EX_glc_e_"] Stacktrace: [1] top-level scope @ ~/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:17 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [3] macro expansion @ ~/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:47 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined] SBML flux model loading: Test Failed at /home/pkgeval/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:53 Expression: ocs[40] == 1.0 Evaluated: 0.0 == 1.0 Stacktrace: [1] top-level scope @ ~/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:17 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [3] macro expansion @ ~/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:53 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined] SBML flux model loading: Test Failed at /home/pkgeval/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:55 Expression: all(ocs .== 0.0) Evaluated: all(Bool[1, 1, 1, 1, 1, 1, 1, 1, 1, 1 … 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]) Stacktrace: [1] top-level scope @ ~/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:17 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [3] macro expansion @ ~/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:55 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined] SBML flux model loading: Test Failed at /home/pkgeval/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:66 Expression: isapprox(lvals[27], uvals[27]) Evaluated: isapprox(-999999.0, 999999.0) Stacktrace: [1] top-level scope @ ~/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:17 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [3] macro expansion @ ~/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:66 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined] SBML flux model loading: Test Failed at /home/pkgeval/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:67 Expression: isapprox(lvals[27], 7.6) Evaluated: isapprox(-999999.0, 7.6) Stacktrace: [1] top-level scope @ ~/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:17 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [3] macro expansion @ ~/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:67 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined] SBML flux model loading: Test Failed at /home/pkgeval/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:68 Expression: isapprox(lvals[12], -10) Evaluated: isapprox(0.0, -10) Stacktrace: [1] top-level scope @ ~/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:17 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [3] macro expansion @ ~/.julia/packages/SBML/mJIpc/test/ecoli_flux.jl:68 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined] ┌ 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 Model Dasgupta2020.xml writes out as expected: Test Failed at /home/pkgeval/.julia/packages/SBML/mJIpc/test/writemodels.jl:48 Expression: #= /home/pkgeval/.julia/packages/SBML/mJIpc/test/writemodels.jl:48 =# @test_logs(writeSBML(model)) == expected Evaluated: "\n\n \n \n \n

a simple kinetic mass-action-law-based model could be utilized to adequately describe clustering in\nresponse to activation both in 2D and in 3D

\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:25:02Z\n \n \n \n \n tiwarik@babraham.ac.uk\n \n \n Tiwari\n Krishna\n \n \n \n \n Babraham Institute\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Tiwari\n Krishna\n \n tiwarik@babraham.ac.uk\n Babraham Institute\n \n \n \n \n 2020-10-30T15:25:02Z\n \n \n 2020-10-30T15:25:02Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:41Z\n \n \n \n \n \n \n \n \n \n k_1 \n \n \n n \n \n \n \n k_1 \n n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:41Z\n \n \n \n \n \n \n \n \n \n k2 \n \n \n p \n \n \n \n k2 \n \n \n p \n 2 \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:40Z\n \n \n \n \n \n \n \n \n \n k2 \n \n \n p \n \n \n \n 2 \n k2 \n \n \n p \n 2 \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:39Z\n \n \n \n \n \n \n \n \n \n k1 \n \n \n n \n \n \n p \n \n \n \n k1 \n n \n p \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:42Z\n \n \n \n \n \n \n \n \n \n k_2 \n \n \n n \n \n \n \n k_2 \n \n \n n \n 2 \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:29:06Z\n \n \n \n \n \n \n \n \n \n \n \n \n 
Concentration of receptor aggregate
\n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:16Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 
Concentration of single receptor/particle
\n \n \n \n \n \n \n \n \n 2020-10-30T15:31:05Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:36Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:48Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:40Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:19Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:44Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:52Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:17Z\n \n \n \n \n \n \n \n \n \n \n \n p0 \n \n \n \n \n \n \n \n \n \n \n ModelValue_6 \n P \n \n N \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:19Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R4_flux \n k2 \n P \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:23Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R5_flux \n k_2 \n N \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:13Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R3_flux \n k_1 \n N \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:27Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n k3 \n N \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:29:18Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R1_flux \n k1 \n N \n P \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:29:21Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R2_flux \n k2 \n P \n \n \n \n \n \n \n \n\n" == "\n\n \n \n \n

a simple kinetic mass-action-law-based model could be utilized to adequately describe clustering in\nresponse to activation both in 2D and in 3D

\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:25:02Z\n \n \n \n \n tiwarik@babraham.ac.uk\n \n \n Tiwari\n Krishna\n \n \n \n \n Babraham Institute\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Tiwari\n Krishna\n \n tiwarik@babraham.ac.uk\n Babraham Institute\n \n \n \n \n 2020-10-30T15:25:02Z\n \n \n 2020-10-30T15:25:02Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:41Z\n \n \n \n \n \n \n \n \n \n k_1 \n \n \n n \n \n \n \n k_1 \n n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:41Z\n \n \n \n \n \n \n \n \n \n k2 \n \n \n p \n \n \n \n k2 \n \n \n p \n 2 \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:42Z\n \n \n \n \n \n \n \n \n \n k_2 \n \n \n n \n \n \n \n k_2 \n \n \n n \n 2 \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:40Z\n \n \n \n \n \n \n \n \n \n k2 \n \n \n p \n \n \n \n 2 \n k2 \n \n \n p \n 2 \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:39Z\n \n \n \n \n \n \n \n \n \n k1 \n \n \n n \n \n \n p \n \n \n \n k1 \n n \n p \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:29:06Z\n \n \n \n \n \n \n \n \n \n \n \n \n 
Concentration of single receptor/particle
\n \n \n \n \n \n \n \n \n 2020-10-30T15:31:05Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 
Concentration of receptor aggregate
\n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:16Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:48Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:19Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:17Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:40Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:36Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:44Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:52Z\n \n \n \n \n \n \n \n \n \n \n \n p0 \n \n \n \n \n \n \n \n \n \n \n ModelValue_6 \n P \n \n N \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:19Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R4_flux \n k2 \n P \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:13Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R3_flux \n k_1 \n N \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:27Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n k3 \n N \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:29:18Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R1_flux \n k1 \n N \n P \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:23Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R5_flux \n k_2 \n N \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:29:21Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R2_flux \n k2 \n P \n \n \n \n \n \n \n \n\n" Stacktrace: [1] top-level scope @ ~/.julia/packages/SBML/mJIpc/test/writemodels.jl:40 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [3] macro expansion @ ~/.julia/packages/SBML/mJIpc/test/writemodels.jl:41 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [5] macro expansion @ ~/.julia/packages/SBML/mJIpc/test/writemodels.jl:48 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined] Model Dasgupta2020.xml writes out as expected: Test Failed at /home/pkgeval/.julia/packages/SBML/mJIpc/test/writemodels.jl:54 Expression: content == expected Evaluated: "\n\n \n \n \n

a simple kinetic mass-action-law-based model could be utilized to adequately describe clustering in\nresponse to activation both in 2D and in 3D

\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:25:02Z\n \n \n \n \n tiwarik@babraham.ac.uk\n \n \n Tiwari\n Krishna\n \n \n \n \n Babraham Institute\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Tiwari\n Krishna\n \n tiwarik@babraham.ac.uk\n Babraham Institute\n \n \n \n \n 2020-10-30T15:25:02Z\n \n \n 2020-10-30T15:25:02Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:41Z\n \n \n \n \n \n \n \n \n \n k_1 \n \n \n n \n \n \n \n k_1 \n n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:41Z\n \n \n \n \n \n \n \n \n \n k2 \n \n \n p \n \n \n \n k2 \n \n \n p \n 2 \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:40Z\n \n \n \n \n \n \n \n \n \n k2 \n \n \n p \n \n \n \n 2 \n k2 \n \n \n p \n 2 \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:39Z\n \n \n \n \n \n \n \n \n \n k1 \n \n \n n \n \n \n p \n \n \n \n k1 \n n \n p \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:42Z\n \n \n \n \n \n \n \n \n \n k_2 \n \n \n n \n \n \n \n k_2 \n \n \n n \n 2 \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:29:06Z\n \n \n \n \n \n \n \n \n \n \n \n \n 
Concentration of receptor aggregate
\n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:16Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 
Concentration of single receptor/particle
\n \n \n \n \n \n \n \n \n 2020-10-30T15:31:05Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:36Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:48Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:40Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:19Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:44Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:52Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:17Z\n \n \n \n \n \n \n \n \n \n \n \n p0 \n \n \n \n \n \n \n \n \n \n \n ModelValue_6 \n P \n \n N \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:19Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R4_flux \n k2 \n P \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:23Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R5_flux \n k_2 \n N \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:13Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R3_flux \n k_1 \n N \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:27Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n k3 \n N \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:29:18Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R1_flux \n k1 \n N \n P \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:29:21Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R2_flux \n k2 \n P \n \n \n \n \n \n \n \n\n" == "\n\n \n \n \n

a simple kinetic mass-action-law-based model could be utilized to adequately describe clustering in\nresponse to activation both in 2D and in 3D

\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:25:02Z\n \n \n \n \n tiwarik@babraham.ac.uk\n \n \n Tiwari\n Krishna\n \n \n \n \n Babraham Institute\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Tiwari\n Krishna\n \n tiwarik@babraham.ac.uk\n Babraham Institute\n \n \n \n \n 2020-10-30T15:25:02Z\n \n \n 2020-10-30T15:25:02Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:41Z\n \n \n \n \n \n \n \n \n \n k_1 \n \n \n n \n \n \n \n k_1 \n n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:41Z\n \n \n \n \n \n \n \n \n \n k2 \n \n \n p \n \n \n \n k2 \n \n \n p \n 2 \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:42Z\n \n \n \n \n \n \n \n \n \n k_2 \n \n \n n \n \n \n \n k_2 \n \n \n n \n 2 \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:40Z\n \n \n \n \n \n \n \n \n \n k2 \n \n \n p \n \n \n \n 2 \n k2 \n \n \n p \n 2 \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:44:39Z\n \n \n \n \n \n \n \n \n \n k1 \n \n \n n \n \n \n p \n \n \n \n k1 \n n \n p \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:29:06Z\n \n \n \n \n \n \n \n \n \n \n \n \n 
Concentration of single receptor/particle
\n \n \n \n \n \n \n \n \n 2020-10-30T15:31:05Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 
Concentration of receptor aggregate
\n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:16Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:48Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:19Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:17Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:40Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:33:36Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:44Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:32:52Z\n \n \n \n \n \n \n \n \n \n \n \n p0 \n \n \n \n \n \n \n \n \n \n \n ModelValue_6 \n P \n \n N \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:19Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R4_flux \n k2 \n P \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:13Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R3_flux \n k_1 \n N \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:27Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n k3 \n N \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:29:18Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R1_flux \n k1 \n N \n P \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:30:23Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R5_flux \n k_2 \n N \n \n \n \n \n \n \n \n \n \n \n \n \n \n 2020-10-30T15:29:21Z\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n Cell \n \n R2_flux \n k2 \n P \n \n \n \n \n \n \n \n\n" Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined] [2] (::var"#53#54"{Model})(filename::String, ::IOStream) @ Main ~/.julia/packages/SBML/mJIpc/test/writemodels.jl:54 [3] mktemp(fn::var"#53#54"{Model}, parent::String) @ Base.Filesystem ./file.jl:907 [4] mktemp(fn::Function) @ Base.Filesystem ./file.jl:905 [5] top-level scope @ ~/.julia/packages/SBML/mJIpc/test/writemodels.jl:40 [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [7] macro expansion @ ~/.julia/packages/SBML/mJIpc/test/writemodels.jl:41 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [9] macro expansion @ ~/.julia/packages/SBML/mJIpc/test/writemodels.jl:49 [inlined] Test Summary: | Pass Fail Broken Total Time SBML test suite | 445 9 1 455 3m52.3s CCall to SBML works and SBML returns a version | 1 1 0.7s Symbolics compatibility | 2 2 12.3s SBML flux model loading | 19 7 26 58.4s Loading of models from various sources - readSBML | 133 133 27.1s Loading of models from various sources - readSBMLFromString | 133 133 11.5s readSBMLFromString | 2 2 0.8s Time variables in math | 1 1 1.6s Units | 5 5 2.0s Initial amounts and concentrations | 8 8 3.6s Initial assignments | 2 2 1.7s Rules | 2 2 1.5s Constraints | 1 1 0.4s Extensive kinetic math | 6 6 3.5s logBase and root math functions | 2 2 2.4s rationals in math | 1 1 0.0s converters work and fail gracefully | 10 10 2.9s relational operators are decoded correctly | 1 1 0.0s custom show | 2 2 9.7s events | 1 1 0.0s model attributes | 21 21 0.0s names and identifiers of objects | 18 18 1.1s constantness | 2 2 0.0s writeSBML | 40 2 42 1m11.2s Model Dasgupta2020.xml writes out as expected | 2 2 4 17.6s Round-trip: e_coli_core.xml | 2 2 7.0s Round-trip: T1M1133.xml | 2 2 21.5s Round-trip: Dasgupta2020.xml | 2 2 0.3s Round-trip: yeast-GEM.xml | 2 2 23.1s Round-trip: 00852-sbml-l3v2.xml | 2 2 0.1s Round-trip: 00140-sbml-l3v2.xml | 2 2 0.1s Round-trip: 00374-sbml-l3v2.xml | 2 2 0.6s Round-trip: 01565-sbml-l3v1.xml | 2 2 0.2s Round-trip: 01289-sbml-l3v2.xml | 2 2 0.0s Round-trip: 00191-sbml-l3v2.xml | 2 2 0.0s Round-trip: 01234-sbml-l3v2.xml | 2 2 0.0s Round-trip: 00489-sbml-l3v2.xml | 2 2 0.0s Round-trip: 00026-sbml-l3v2.xml | 2 2 0.0s Round-trip: 00983-sbml-l3v2.xml | 2 2 0.1s Round-trip: 00054-sbml-l3v2.xml | 2 2 0.0s Round-trip: 00975-sbml-l3v2.xml | 2 2 0.0s Round-trip: 00976-sbml-l3v2.xml | 2 2 0.0s Round-trip: 01323-sbml-l3v2.xml | 2 2 0.1s Round-trip: 00878-sbml-l3v2.xml | 2 2 0.0s Loading of models from sbml_test_suite | 23 1 24 1.6s Math interpretation | 9 9 1.6s RNG of the outermost testset: Random.Xoshiro(0x5e43232b078c4d4c, 0x101826c8ec1c7e47, 0x7a9ab75eeb46b8d2, 0x6b2a5917f5464496, 0xe1b99c08192f4455) ERROR: LoadError: Some tests did not pass: 445 passed, 9 failed, 0 errored, 1 broken. in expression starting at /home/pkgeval/.julia/packages/SBML/mJIpc/test/runtests.jl:21 Testing failed after 217.54s ERROR: LoadError: Package SBML errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/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/v1.14/Pkg/src/Operations.jl:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [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/v1.14/Pkg/src/API.jl:586 [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/v1.14/Pkg/src/API.jl:562 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:323 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1477.97s: package fails to precompile