Package evaluation to test COBREXA on Julia 1.14.0-DEV.3081 (21a70e450d*) started at 2026-09-02T00:23:04.696 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 31.12s ################################################################################ # Installation # Installing COBREXA... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [babc4406] + COBREXA v2.9.1 Updating `~/.julia/environments/v1.14/Manifest.toml` [5a4f3dfa] + AbstractFBCModels v1.4.0 [babc4406] + COBREXA v2.9.1 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.9 [bbf7d656] + CommonSubexpressions v0.3.1 [5515826b] + ConstraintTrees v1.11.1 [187b0558] + ConstructionBase v1.6.0 [864edb3b] + DataStructures v0.19.6 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.16.0 [ffbed154] + DocStringExtensions v0.9.5 [f6369f11] + ForwardDiff v1.4.5 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.8.0 [682c06a0] + JSON v1.7.1 [4076af6c] + JuMP v1.31.2 [2ab3a3ac] + LogExpFunctions v1.0.1 [1914dd2f] + MacroTools v0.5.16 [b8f27783] + MathOptInterface v1.53.0 [d8a4904e] + MutableArithmetics v1.8.0 [77ba4419] + NaNMath v1.1.4 [bac558e1] + OrderedCollections v2.0.1 ⌅ [69de0a69] + Parsers v2.8.7 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [276daf66] + SpecialFunctions v2.9.0 [860ef19b] + StableRNGs v1.0.4 [1e83bf80] + StaticArraysCore v1.4.4 [ec057cc2] + StructUtils v2.8.5 [3bb67fe8] + TranscodingStreams v0.11.3 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [0dad84c5] + ArgTools v1.2.0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.12.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching 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 v1.14.0 [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 v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [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 v1.5.7+0 [deac9b47] + LibCURL_jll v8.21.0+0 [e37daf67] + LibGit2_jll v1.9.7+0 [29816b5a] + LibSSH2_jll v1.11.104+0 [14a3606d] + MozillaCACerts_jll v2026.8.13 [4536629a] + OpenBLAS_jll v0.3.34+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.8+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 v1.70.0+0 [3f19e933] + p7zip_jll v17.8.2+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 5.01s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 3.3 s ✓ SBML_jll 10.3 s ✓ JSONFBCModels 153.7 s ✓ Clarabel 22.1 s ✓ COBREXA 16.1 s ✓ SBML 3.7 s ✓ SBMLFBCModels 6 dependencies successfully precompiled in 225 seconds. 119 already precompiled. Precompilation completed after 220.93s ################################################################################ # Testing # Testing COBREXA Status `/tmp/jl_zR4Snz/Project.toml` [5a4f3dfa] AbstractFBCModels v1.4.0 ⌅ [4c88cf16] Aqua v0.7.4 [babc4406] COBREXA v2.9.1 [336ed68f] CSV v0.10.17 ⌅ [61c947e1] Clarabel v0.6.0 [5515826b] ConstraintTrees v1.11.1 [ffbed154] DocStringExtensions v0.9.5 [87dc4568] HiGHS v1.25.1 [475c1105] JSONFBCModels v1.1.0 [4076af6c] JuMP v1.31.2 [3e8f9d1a] SBMLFBCModels v1.1.1 [860ef19b] StableRNGs v1.0.4 [6dd1b50a] Tulip v0.9.8 [8ba89e20] Distributed v1.12.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.14.0 [44cfe95a] Pkg v1.14.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.13.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_zR4Snz/Manifest.toml` [14f7f29c] AMD v0.5.3 [5a4f3dfa] AbstractFBCModels v1.4.0 ⌅ [4c88cf16] Aqua v0.7.4 [babc4406] COBREXA v2.9.1 [336ed68f] CSV v0.10.17 ⌅ [61c947e1] Clarabel v0.6.0 [523fee87] CodecBzip2 v0.8.5 [944b1d66] CodecZlib v0.7.9 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.1 [5515826b] ConstraintTrees v1.11.1 [187b0558] ConstructionBase v1.6.0 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.6 [e2d170a0] DataValueInterfaces v1.0.0 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.16.0 [ffbed154] DocStringExtensions v0.9.5 [e2ba6199] ExprTools v0.1.11 [9aa1b823] FastClosures v0.3.2 [48062228] FilePathsBase v0.9.24 [f6369f11] ForwardDiff v1.4.5 ⌅ [14197337] GenericLinearAlgebra v0.3.19 [87dc4568] HiGHS v1.25.1 [615f187c] IfElse v0.1.1 [842dd82b] InlineStrings v1.4.5 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [682c06a0] JSON v1.7.1 [475c1105] JSONFBCModels v1.1.0 [4076af6c] JuMP v1.31.2 [ba0b0d4f] Krylov v0.10.9 [40e66cde] LDLFactorizations v0.10.2 [5c8ed15e] LinearOperators v2.14.2 [2ab3a3ac] LogExpFunctions v1.0.1 [1914dd2f] MacroTools v0.5.16 [8c4f8055] MathOptIIS v0.2.0 [b8f27783] MathOptInterface v1.53.0 [d8a4904e] MutableArithmetics v1.8.0 [77ba4419] NaNMath v1.1.4 [bac558e1] OrderedCollections v2.0.1 ⌅ [69de0a69] Parsers v2.8.7 [3bbf5609] PikaParser v0.6.1 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [bfc457fd] QDLDL v0.4.1 [10f199a5] QPSReader v0.2.1 [ae029012] Requires v1.3.1 [e5567a89] SBML v1.6.0 [3e8f9d1a] SBMLFBCModels v1.1.1 [91c51154] SentinelArrays v1.4.10 [66db9d55] SnoopPrecompile v1.0.3 [276daf66] SpecialFunctions v2.9.0 [860ef19b] StableRNGs v1.0.4 [90137ffa] StaticArrays v1.9.19 [1e83bf80] StaticArraysCore v1.4.4 [ec057cc2] StructUtils v2.8.5 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.14.0 ⌅ [a759f4b9] TimerOutputs v0.5.29 [3bb67fe8] TranscodingStreams v0.11.3 [6dd1b50a] Tulip v0.9.8 [1986cc42] Unitful v1.28.0 [ea10d353] WeakRefStrings v1.4.3 [76eceee3] WorkerUtilities v1.6.1 [6e34b625] Bzip2_jll v1.0.9+0 [8fd58aa0] HiGHS_jll v1.15.1+1 [94ce4f54] Libiconv_jll v1.18.0+0 [656ef2d0] OpenBLAS32_jll v0.3.34+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [bb12108a] SBML_jll v5.21.0+0 ⌅ [02c8fc9c] XML2_jll v2.13.9+0 [0dad84c5] ArgTools v1.2.0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.12.0 [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 v1.14.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap 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 v1.13.0 [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 v1.5.7+0 [deac9b47] LibCURL_jll v8.21.0+0 [e37daf67] LibGit2_jll v1.9.7+0 [29816b5a] LibSSH2_jll v1.11.104+0 [14a3606d] MozillaCACerts_jll v2026.8.13 [4536629a] OpenBLAS_jll v0.3.34+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.8+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 v1.70.0+0 [3f19e933] p7zip_jll v17.8.2+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: `disable_sigint` no longer defers Ctrl-C: SIGINT is delivered as a cancellation of the current ^C scope and observed at cancellation points regardless of the sigatomic region this establishes. Shield a region from cancellation by scoping `Base.CANCEL_TOKEN => nothing` over it instead. │ caller = optimize!(model::HiGHS.Optimizer) at MOI_wrapper.jl:2314 â”” @ HiGHS ~/.julia/packages/HiGHS/erykA/src/MOI_wrapper.jl:2314 ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. │ caller = _delete!(h::OrderedCollections.OrderedDict{HiGHS._ConstraintKey, HiGHS._ConstraintInfo}, index::Int64) at ordered_dict.jl:455 [inlined] â”” @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:455 ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. │ caller = _delete!(h::OrderedCollections.OrderedDict{HiGHS._ConstraintKey, HiGHS._ConstraintInfo}, index::Int64) at ordered_dict.jl:456 [inlined] â”” @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:456 ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. │ caller = _delete!(h::OrderedCollections.OrderedDict{MathOptInterface.ConstraintIndex{MathOptInterface.ScalarAffineFunction{Float64}, MathOptInterface.Interval{Float64}}, Tuple{MathOptInterface.ScalarAffineFunction{Float64}, MathOptInterface.Interval{Float64}}}, index::Int64) at ordered_dict.jl:455 [inlined] â”” @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:455 ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. │ caller = _delete!(h::OrderedCollections.OrderedDict{MathOptInterface.ConstraintIndex{MathOptInterface.ScalarAffineFunction{Float64}, MathOptInterface.Interval{Float64}}, Tuple{MathOptInterface.ScalarAffineFunction{Float64}, MathOptInterface.Interval{Float64}}}, index::Int64) at ordered_dict.jl:456 [inlined] â”” @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:456 [ Info: misc.jl done in 95.68s {"genes":[{"annotation":{"asap":["ABE-0000027"],"ecogene":["EG11556"],"ncbigene":["944748"],"ncbigi"... 7JL5Model |“)Œ&i!‚ø@‰ú=OZAbstractFBCModelsCanonicalModelD5DictNžD!Reaction... {"genes":[{"annotation":{"asap":["ABE-0000027"],"ecogene":["EG11556"],"ncbigene":["944748"],"ncbigi"... [ Info: ../docs/src/examples/01-loading-and-saving.jl done in 68.81s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/02a-flux-balance-analysis.jl done in 6.04s [ 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 85.02s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/02c-model-modifications.jl done in 4.81s [ Info: using cached `e_coli_core.json' nothing[ Info: ../docs/src/examples/02d-constraint-modifications.jl done in 0.28s [ Info: using cached `e_coli_core.json' From worker 3: ┌ Warning: `disable_sigint` no longer defers Ctrl-C: SIGINT is delivered as a cancellation of the current ^C scope and observed at cancellation points regardless of the sigatomic region this establishes. Shield a region from cancellation by scoping `Base.CANCEL_TOKEN => nothing` over it instead. From worker 3: │ caller = optimize!(model::HiGHS.Optimizer) at MOI_wrapper.jl:2314 From worker 3: â”” @ HiGHS ~/.julia/packages/HiGHS/erykA/src/MOI_wrapper.jl:2314 From worker 2: ┌ Warning: `disable_sigint` no longer defers Ctrl-C: SIGINT is delivered as a cancellation of the current ^C scope and observed at cancellation points regardless of the sigatomic region this establishes. Shield a region from cancellation by scoping `Base.CANCEL_TOKEN => nothing` over it instead. From worker 2: │ caller = optimize!(model::HiGHS.Optimizer) at MOI_wrapper.jl:2314 From worker 2: â”” @ HiGHS ~/.julia/packages/HiGHS/erykA/src/MOI_wrapper.jl:2314 [ Info: ../docs/src/examples/03a-flux-variability-analysis.jl done in 146.59s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03b-parsimonious-flux-balance.jl done in 208.27s [ Info: using cached `e_coli_core.json' From worker 2: ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. From worker 2: │ caller = _delete!(h::OrderedCollections.OrderedDict{HiGHS._ConstraintKey, HiGHS._ConstraintInfo}, index::Int64) at ordered_dict.jl:455 [inlined] From worker 2: â”” @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:455 From worker 2: ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. From worker 2: │ caller = _delete!(h::OrderedCollections.OrderedDict{HiGHS._ConstraintKey, HiGHS._ConstraintInfo}, index::Int64) at ordered_dict.jl:456 [inlined] From worker 2: â”” @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:456 From worker 3: ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. From worker 3: │ caller = _delete!(h::OrderedCollections.OrderedDict{HiGHS._ConstraintKey, HiGHS._ConstraintInfo}, index::Int64) at ordered_dict.jl:455 [inlined] From worker 3: â”” @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:455 From worker 2: ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. From worker 2: │ caller = _delete!(h::OrderedCollections.OrderedDict{MathOptInterface.ConstraintIndex{MathOptInterface.ScalarAffineFunction{Float64}, MathOptInterface.EqualTo{Float64}}, Tuple{MathOptInterface.ScalarAffineFunction{Float64}, MathOptInterface.EqualTo{Float64}}}, index::Int64) at ordered_dict.jl:455 [inlined] From worker 2: â”” @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:455 From worker 3: ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. From worker 3: │ caller = _delete!(h::OrderedCollections.OrderedDict{HiGHS._ConstraintKey, HiGHS._ConstraintInfo}, index::Int64) at ordered_dict.jl:456 [inlined] From worker 3: â”” @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:456 From worker 2: ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. From worker 2: │ caller = _delete!(h::OrderedCollections.OrderedDict{MathOptInterface.ConstraintIndex{MathOptInterface.ScalarAffineFunction{Float64}, MathOptInterface.EqualTo{Float64}}, Tuple{MathOptInterface.ScalarAffineFunction{Float64}, MathOptInterface.EqualTo{Float64}}}, index::Int64) at ordered_dict.jl:456 [inlined] From worker 2: â”” @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:456 From worker 3: ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. From worker 3: │ caller = _delete!(h::OrderedCollections.OrderedDict{MathOptInterface.ConstraintIndex{MathOptInterface.ScalarAffineFunction{Float64}, MathOptInterface.EqualTo{Float64}}, Tuple{MathOptInterface.ScalarAffineFunction{Float64}, MathOptInterface.EqualTo{Float64}}}, index::Int64) at ordered_dict.jl:455 [inlined] From worker 3: â”” @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:455 From worker 3: ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. From worker 3: │ caller = _delete!(h::OrderedCollections.OrderedDict{MathOptInterface.ConstraintIndex{MathOptInterface.ScalarAffineFunction{Float64}, MathOptInterface.EqualTo{Float64}}, Tuple{MathOptInterface.ScalarAffineFunction{Float64}, MathOptInterface.EqualTo{Float64}}}, index::Int64) at ordered_dict.jl:456 [inlined] From worker 3: â”” @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:456 [ Info: ../docs/src/examples/03c-envelopes.jl done in 17.15s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03d-unidirectional.jl done in 9.63s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/03e-min-exchange.jl done in 14.58s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/04-community-models.jl done in 110.41s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/04a-composition-models.jl done in 4.35s [ Info: using cached `e_coli_core.json' docs/05a-minimization-of-metabolic-adjustment.jl: Error During Test at /home/pkgeval/.julia/packages/COBREXA/9nHZI/test/runtests.jl:40 Got exception outside of a @test LoadError: UndefRefError: access to undefined reference Stacktrace: [1] getproperty(x::DataStructures.KDRec{Symbol, Nothing}, f::Symbol) @ Base Base_compiler.jl:58 [inlined] [2] DataStructures.BalancedTree23{Symbol, Nothing, Base.Order.ForwardOrdering}(::Val{true}, iterable::Base.Generator{DataStructures.IntersectTwoSortedSets{Symbol, Base.Order.ForwardOrdering}, DataStructures.var"#82#83"}, ord::Base.Order.ForwardOrdering, allowdups::Bool) @ DataStructures ~/.julia/packages/DataStructures/IwRP2/src/balanced_tree.jl:1053 [3] (DataStructures.SortedSet{Symbol})(::Val{true}, iterable::DataStructures.IntersectTwoSortedSets{Symbol, Base.Order.ForwardOrdering}, ord::Base.Order.ForwardOrdering) @ DataStructures ~/.julia/packages/DataStructures/IwRP2/src/sorted_set.jl:82 [inlined] [4] intersect2(m1::DataStructures.SortedSet{Symbol, Base.Order.ForwardOrdering}, m2::DataStructures.SortedSet{Symbol, Base.Order.ForwardOrdering}) @ DataStructures ~/.julia/packages/DataStructures/IwRP2/src/sorted_set.jl:425 [inlined] [5] intersect(m1::DataStructures.SortedSet{Symbol, Base.Order.ForwardOrdering}, others::DataStructures.SortedSet{Symbol, Base.Order.ForwardOrdering}) @ DataStructures ~/.julia/packages/DataStructures/IwRP2/src/sorted_set.jl:458 [inlined] [6] (::ConstraintTrees.var"#go#zip##0"{Float64, typeof(-)})(x::ConstraintTrees.Tree{Float64}, y::ConstraintTrees.Tree{Float64}) @ ConstraintTrees ~/.julia/packages/ConstraintTrees/WXXYD/src/tree.jl:377 [7] (::ConstraintTrees.var"#zip##1#zip##2"{ConstraintTrees.Tree{Float64}, ConstraintTrees.Tree{Float64}})(k::Symbol) @ ConstraintTrees ~/.julia/packages/ConstraintTrees/WXXYD/src/tree.jl:377 [8] iterate(::Base.Generator{DataStructures.SortedSet{Symbol, Base.Order.ForwardOrdering}, ConstraintTrees.var"#zip##1#zip##2"{ConstraintTrees.Tree{Float64}, ConstraintTrees.Tree{Float64}}}) @ Base generator.jl:49 [inlined] [9] DataStructures.SortedDict{Symbol, Union{Float64, ConstraintTrees.Tree{Float64}}, Base.Order.ForwardOrdering}(o::Base.Order.ForwardOrdering, kv::Base.Generator{DataStructures.SortedSet{Symbol, Base.Order.ForwardOrdering}, ConstraintTrees.var"#zip##1#zip##2"{ConstraintTrees.Tree{Float64}, ConstraintTrees.Tree{Float64}}}) @ DataStructures ~/.julia/packages/DataStructures/IwRP2/src/sorted_dict.jl:24 [10] (DataStructures.SortedDict{Symbol, Union{Float64, ConstraintTrees.Tree{Float64}}})(iter::Base.Generator{DataStructures.SortedSet{Symbol, Base.Order.ForwardOrdering}, ConstraintTrees.var"#zip##1#zip##2"{ConstraintTrees.Tree{Float64}, ConstraintTrees.Tree{Float64}}}, o::Base.Order.ForwardOrdering) @ DataStructures ~/.julia/packages/DataStructures/IwRP2/src/sorted_dict.jl:86 [inlined] [11] (DataStructures.SortedDict{Symbol, Union{Float64, ConstraintTrees.Tree{Float64}}})(iter::Base.Generator{DataStructures.SortedSet{Symbol, Base.Order.ForwardOrdering}, ConstraintTrees.var"#zip##1#zip##2"{ConstraintTrees.Tree{Float64}, ConstraintTrees.Tree{Float64}}}) @ DataStructures ~/.julia/packages/DataStructures/IwRP2/src/sorted_dict.jl:86 [inlined] [12] ConstraintTrees.Tree{Float64}(x::Base.Generator{DataStructures.SortedSet{Symbol, Base.Order.ForwardOrdering}, ConstraintTrees.var"#zip##1#zip##2"{ConstraintTrees.Tree{Float64}, ConstraintTrees.Tree{Float64}}}) @ ConstraintTrees ~/.julia/packages/ConstraintTrees/WXXYD/src/tree.jl:35 [inlined] [13] (::ConstraintTrees.var"#go#zip##0"{Float64, typeof(-)})(x::ConstraintTrees.Tree{Float64}, y::ConstraintTrees.Tree{Float64}) @ ConstraintTrees ~/.julia/packages/ConstraintTrees/WXXYD/src/tree.jl:377 [14] zip(f::typeof(-), x::ConstraintTrees.Tree{Float64}, y::ConstraintTrees.Tree{Float64}, ::Core.TypeEgal{Float64}) @ ConstraintTrees ~/.julia/packages/ConstraintTrees/WXXYD/src/tree.jl:382 [15] top-level scope @ ~/.julia/packages/COBREXA/9nHZI/docs/src/examples/05a-minimization-of-metabolic-adjustment.jl:84 [16] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:335 [17] macro expansion @ timing.jl:505 [inlined] [18] run_test_file(path::String) @ Main ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:34 [inlined] [19] macro expansion @ ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:41 [inlined] [20] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined] [21] run_doc_examples() @ Main ~/.julia/packages/COBREXA/9nHZI/test/runtests.jl:41 in expression starting at /home/pkgeval/.julia/packages/COBREXA/9nHZI/docs/src/examples/05a-minimization-of-metabolic-adjustment.jl:84 [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05b-enzyme-constrained-models.jl done in 19.26s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05c-mmdf.jl done in 6.68s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05d-loopless-models.jl done in 6.28s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05e-knockouts.jl done in 23.93s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/05f-cyclefree.jl done in 43.45s [ Info: using cached `e_coli_core.json' nothing [ Info: ../docs/src/examples/05g-gapfilling.jl done in 6.07s [ Info: using cached `e_coli_core.json' nothing [ Info: ../docs/src/examples/05h-medium.jl done in 3.2s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/06a-sampling.jl done in 8.35s [ Info: using cached `e_coli_core.json' [ Info: ../docs/src/examples/06b-screening.jl done in 9.38s [ Info: ../docs/src/examples/07a-srba.jl done in 76.8s [ Info: using cached `iML1515.json' [ Info: ../docs/src/examples/07b-community-ecfba.jl done in 17.73s ┌ 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”” @ Aqua ~/.julia/packages/Aqua/rmHe1/src/exports.jl:5 [ Info: aqua.jl done in 20.01s Test Summary: | Pass Error Total Time COBREXA test suite | 110 1 111 16m60.0s Miscellaneous tests | 39 39 1m35.9s docs/01-loading-and-saving.jl | 1 1 1m08.8s docs/02a-flux-balance-analysis.jl | 1 1 6.0s docs/02b-optimizer-parameters.jl | 2 2 1m25.0s docs/02c-model-modifications.jl | 4 4 4.8s docs/02d-constraint-modifications.jl | 2 2 0.3s docs/03a-flux-variability-analysis.jl | 2 2 2m26.6s docs/03b-parsimonious-flux-balance.jl | 6 6 3m28.3s docs/03c-envelopes.jl | 1 1 17.1s docs/03d-unidirectional.jl | 6 6 9.6s docs/03e-min-exchange.jl | 1 1 14.6s docs/04-community-models.jl | 3 3 1m50.4s docs/04a-composition-models.jl | 7 7 4.4s docs/05a-minimization-of-metabolic-adjustment.jl | 3 1 4 4.1s docs/05b-enzyme-constrained-models.jl | 7 7 19.3s docs/05c-mmdf.jl | 5 5 6.7s docs/05d-loopless-models.jl | 1 1 6.3s docs/05e-knockouts.jl | 5 5 23.9s docs/05f-cyclefree.jl | 0 43.5s docs/05g-gapfilling.jl | 2 2 6.1s docs/05h-medium.jl | 3 3 3.2s docs/06a-sampling.jl | 1 1 8.4s docs/06b-screening.jl | 0 9.4s docs/07a-srba.jl | 1 1 1m19.0s docs/07b-community-ecfba.jl | 1 1 17.7s Automated QUality Assurance | 6 6 16.0s RNG of the outermost testset: Random.Xoshiro(0xdd81574d1c40f86c, 0xa7e11016d6a12bda, 0x0dc4327c3555fd33, 0x7c78bb909bde792d, 0x8146a4f2ede7be34) ERROR: LoadError: Some tests did not pass: 110 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/COBREXA/9nHZI/test/runtests.jl:58 Testing failed after 988.09s ERROR: LoadError: Package COBREXA 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:3283 [3] 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:587 [4] 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 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1516.44s: package tests unexpectedly errored