Package evaluation of COBREXA on Julia 1.13.0-DEV.582 (c0a1728d50*) started at 2025-05-14T14:03:35.492 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.52s ################################################################################ # Installation # Installing COBREXA... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [babc4406] + COBREXA v2.8.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [5a4f3dfa] + AbstractFBCModels v1.3.0 [6e4b80f9] + BenchmarkTools v1.6.0 [babc4406] + COBREXA v2.8.0 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.16.0 [5515826b] + ConstraintTrees v1.9.0 [187b0558] + ConstructionBase v1.5.8 [864edb3b] + DataStructures v0.18.22 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [ffbed154] + DocStringExtensions v0.9.4 [f6369f11] + ForwardDiff v1.0.1 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [0f8b85d8] + JSON3 v1.14.2 [4076af6c] + JuMP v1.25.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [b8f27783] + MathOptInterface v1.40.0 [d8a4904e] + MutableArithmetics v1.6.4 [77ba4419] + NaNMath v1.1.3 [bac558e1] + OrderedCollections v1.8.0 [69de0a69] + Parsers v2.8.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [276daf66] + SpecialFunctions v2.5.1 [860ef19b] + StableRNGs v1.0.3 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [856f2bd8] + StructTypes v1.11.0 [3bb67fe8] + TranscodingStreams v0.11.3 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+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 [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 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [9abbd945] + Profile 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 [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 v8.12.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.2.25 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Installation completed after 4.11s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 39.73s ################################################################################ # Testing # Testing COBREXA Status `/tmp/jl_SH04j5/Project.toml` [5a4f3dfa] AbstractFBCModels v1.3.0 ⌅ [4c88cf16] Aqua v0.7.4 [babc4406] COBREXA v2.8.0 [336ed68f] CSV v0.10.15 ⌅ [61c947e1] Clarabel v0.6.0 [5515826b] ConstraintTrees v1.9.0 [ffbed154] DocStringExtensions v0.9.4 [87dc4568] HiGHS v1.17.0 [475c1105] JSONFBCModels v1.0.0 [4076af6c] JuMP v1.25.0 [3e8f9d1a] SBMLFBCModels v1.1.0 [860ef19b] StableRNGs v1.0.3 [6dd1b50a] Tulip v0.9.7 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.12.0 [44cfe95a] Pkg v1.13.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [2f01184e] SparseArrays v1.12.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_SH04j5/Manifest.toml` [14f7f29c] AMD v0.5.3 [5a4f3dfa] AbstractFBCModels v1.3.0 ⌅ [4c88cf16] Aqua v0.7.4 [6e4b80f9] BenchmarkTools v1.6.0 [babc4406] COBREXA v2.8.0 [336ed68f] CSV v0.10.15 ⌅ [61c947e1] Clarabel v0.6.0 [523fee87] CodecBzip2 v0.8.5 [944b1d66] CodecZlib v0.7.8 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.16.0 [5515826b] ConstraintTrees v1.9.0 [187b0558] ConstructionBase v1.5.8 [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 [ffbed154] DocStringExtensions v0.9.4 [e2ba6199] ExprTools v0.1.10 [9aa1b823] FastClosures v0.3.2 [48062228] FilePathsBase v0.9.24 [f6369f11] ForwardDiff v1.0.1 [14197337] GenericLinearAlgebra v0.3.17 [87dc4568] HiGHS v1.17.0 [615f187c] IfElse v0.1.1 [842dd82b] InlineStrings v1.4.3 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.2 [475c1105] JSONFBCModels v1.0.0 [4076af6c] JuMP v1.25.0 ⌅ [ba0b0d4f] Krylov v0.9.10 [40e66cde] LDLFactorizations v0.10.1 [5c8ed15e] LinearOperators v2.10.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [b8f27783] MathOptInterface v1.40.0 [d8a4904e] MutableArithmetics v1.6.4 [77ba4419] NaNMath v1.1.3 [bac558e1] OrderedCollections v1.8.0 [69de0a69] Parsers v2.8.3 [3bbf5609] PikaParser v0.6.1 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [bfc457fd] QDLDL v0.4.1 [10f199a5] QPSReader v0.2.1 [ae029012] Requires v1.3.1 [e5567a89] SBML v1.6.0 [3e8f9d1a] SBMLFBCModels v1.1.0 [91c51154] SentinelArrays v1.4.8 [66db9d55] SnoopPrecompile v1.0.3 [276daf66] SpecialFunctions v2.5.1 [860ef19b] StableRNGs v1.0.3 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [856f2bd8] StructTypes v1.11.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [a759f4b9] TimerOutputs v0.5.28 [3bb67fe8] TranscodingStreams v0.11.3 [6dd1b50a] Tulip v0.9.7 [1986cc42] Unitful v1.22.1 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [6e34b625] Bzip2_jll v1.0.9+0 [8fd58aa0] HiGHS_jll v1.10.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+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 v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [9abbd945] Profile 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 v8.12.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.2.25 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... 142270.9 ms ✓ Clarabel 1 dependency successfully precompiled in 143 seconds. 62 already precompiled. Precompiling packages... 18830.8 ms ✓ Tulip 1 dependency successfully precompiled in 20 seconds. 76 already precompiled. [ Info: misc.jl done in 57.42s Precompiling packages... 8581.0 ms ✓ JSONFBCModels 1 dependency successfully precompiled in 9 seconds. 33 already precompiled. Precompiling packages... 1816.3 ms ✓ SBML_jll 18782.7 ms ✓ SBML 5181.7 ms ✓ SBMLFBCModels 3 dependencies successfully precompiled in 26 seconds. 32 already precompiled. {"reactions":[{"name":"Acetaldehyde dehydrogenase (acetylating)","upper_bound":1000.0,"objective_coe... 7JL5Model |“)Œ&i!‚ø@‰ú=OZAbstractFBCModelsCanonicalModelD5DictNžD!Reaction... {"reactions":[{"name":"Acetaldehyde dehydrogenase (acetylating)","upper_bound":1000.0,"objective_coe... [ Info: ../docs/src/examples/01-loading-and-saving.jl done in 98.39s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/02a-flux-balance-analysis.jl done in 7.43s [ Info: using cached `e_coli_core.json' nothing Problem info Name : Constraints : 262 Variables : 95 Non-zeros : 550 Reduced problem info Constraints : 62 (removed 200) Variables : 81 (removed 14) Non-zeros : 325 (removed 225) Presolve time : 0.000s Optimizer info (HSD) Constraints : 62 Variables : 81 RHS : [+0.00e+00, +0.00e+00] Lower bounds : [-2.32e+03, +1.25e+01] Upper bounds : [+0.00e+00, +1.16e+04] Linear solver options Arithmetic : Float64 Backend : CHOLMOD System : Augmented system (K2) Itn PObj DObj PFeas DFeas GFeas Mu Time 0 -0.0000000e+00 +1.7686535e+05 1.16e+04 8.59e-02 1.77e+05 1.0e+00 2.65 Solver exited with status Trm_TimeLimit [ Info: ../docs/src/examples/02b-optimizer-parameters.jl done in 95.11s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/02c-model-modifications.jl done in 4.32s [ Info: using cached `e_coli_core.json' nothing[ Info: ../docs/src/examples/02d-constraint-modifications.jl done in 0.19s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03a-flux-variability-analysis.jl done in 100.07s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03b-parsimonious-flux-balance.jl done in 176.95s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03c-envelopes.jl done in 16.46s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03d-unidirectional.jl done in 8.01s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/04-community-models.jl done in 98.69s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/04a-composition-models.jl done in 5.86s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05a-minimization-of-metabolic-adjustment.jl done in 4.38s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05b-enzyme-constrained-models.jl done in 18.86s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05c-mmdf.jl done in 8.52s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05d-loopless-models.jl done in 7.83s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05e-knockouts.jl done in 30.87s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05f-cyclefree.jl done in 50.13s [ Info: using cached `e_coli_core.json' nothing [ Info: ../docs/src/examples/05g-gapfilling.jl done in 6.29s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/06a-sampling.jl done in 8.92s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/06b-screening.jl done in 12.18s Precompiling packages... 31605.3 ms ✓ CSV 1 dependency successfully precompiled in 32 seconds. 29 already precompiled. docs/07a-srba.jl: Test Failed at /home/pkgeval/.julia/packages/COBREXA/1Pbwx/docs/src/examples/07a-srba.jl:351 Expression: isapprox(res.total_capacity, 538.778495150974, atol = TEST_TOLERANCE) Evaluated: isapprox(0.0, 538.778495150974; atol = 0.001) Stacktrace: [1] top-level scope @ ~/.julia/packages/COBREXA/1Pbwx/docs/src/examples/07a-srba.jl:518 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [3] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [4] IncludeInto @ ./Base.jl:311 [inlined] [5] macro expansion @ ./timing.jl:461 [inlined] [6] run_test_file @ ~/.julia/packages/COBREXA/1Pbwx/test/runtests.jl:34 [inlined] [7] macro expansion @ ~/.julia/packages/COBREXA/1Pbwx/test/runtests.jl:41 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [9] run_doc_examples() @ Main ~/.julia/packages/COBREXA/1Pbwx/test/runtests.jl:41 [ Info: ../docs/src/examples/07a-srba.jl done in 122.0s [ Info: using cached `iML1515.json' docs/07b-community-ecfba.jl: Test Failed at /home/pkgeval/.julia/packages/COBREXA/1Pbwx/docs/src/examples/07b-community-ecfba.jl:172 Expression: isapprox(res.community_biomass, 0.2304879809596633, atol = TEST_TOLERANCE) Evaluated: isapprox(26.07967510596681, 0.2304879809596633; atol = 0.001) Stacktrace: [1] top-level scope @ ~/.julia/packages/COBREXA/1Pbwx/docs/src/examples/07b-community-ecfba.jl:518 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:730 [inlined] [3] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [4] IncludeInto @ ./Base.jl:311 [inlined] [5] macro expansion @ ./timing.jl:461 [inlined] [6] run_test_file @ ~/.julia/packages/COBREXA/1Pbwx/test/runtests.jl:34 [inlined] [7] macro expansion @ ~/.julia/packages/COBREXA/1Pbwx/test/runtests.jl:41 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] [9] run_doc_examples() @ Main ~/.julia/packages/COBREXA/1Pbwx/test/runtests.jl:41 [ Info: ../docs/src/examples/07b-community-ecfba.jl done in 10.63s ┌ Warning: `isbindingresolved(m::Module, var::Symbol)` is deprecated, use `true` instead. │ caller = walkmodules(f::Aqua.var"#undefined_exports##0#undefined_exports##1"{Vector{Symbol}}, x::Module) at exports.jl:5 â”” @ Core ~/.julia/packages/Aqua/rmHe1/src/exports.jl:5 [ Info: aqua.jl done in 101.81s Test Summary: | Pass Fail Total Time COBREXA test suite | 101 2 103 17m34.5s Miscellaneous tests | 32 32 57.7s docs/01-loading-and-saving.jl | 1 1 1m38.4s docs/02a-flux-balance-analysis.jl | 1 1 7.4s docs/02b-optimizer-parameters.jl | 2 2 1m35.1s docs/02c-model-modifications.jl | 4 4 4.3s docs/02d-constraint-modifications.jl | 2 2 0.2s docs/03a-flux-variability-analysis.jl | 2 2 1m40.1s docs/03b-parsimonious-flux-balance.jl | 6 6 2m57.0s docs/03c-envelopes.jl | 1 1 16.5s docs/03d-unidirectional.jl | 6 6 8.0s docs/04-community-models.jl | 3 3 1m38.7s docs/04a-composition-models.jl | 7 7 5.9s docs/05a-minimization-of-metabolic-adjustment.jl | 7 7 4.4s docs/05b-enzyme-constrained-models.jl | 7 7 18.9s docs/05c-mmdf.jl | 5 5 8.5s docs/05d-loopless-models.jl | 1 1 7.8s docs/05e-knockouts.jl | 5 5 30.9s docs/05f-cyclefree.jl | 0 50.1s docs/05g-gapfilling.jl | 2 2 6.3s docs/06a-sampling.jl | 1 1 8.9s docs/06b-screening.jl | 0 12.2s docs/07a-srba.jl | 1 1 2m04.6s docs/07b-community-ecfba.jl | 1 1 10.6s Automated QUality Assurance | 6 6 1m41.7s RNG of the outermost testset: Random.Xoshiro(0x216263198e9e573f, 0x5adbcb8321a68475, 0x53cbed14cba31617, 0xc75142987b1e5fce, 0x482a39364b95f1b3) ERROR: LoadError: Some tests did not pass: 101 passed, 2 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/COBREXA/1Pbwx/test/runtests.jl:58 Testing failed after 1336.52s ERROR: LoadError: Package COBREXA 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:2418 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2273 [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:498 [5] 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:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:151 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:309 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:331 [12] _start() @ Base ./client.jl:564 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1416.18s: package has test failures