Package evaluation of JSONFBCModels on Julia 1.13.0-DEV.896 (efa4faf9a4*) started at 2025-07-25T12:30:31.065 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 13.68s ################################################################################ # Installation # Installing JSONFBCModels... Resolving package versions... Installed DocStringExtensions ─ v0.9.5 Installed JSON ──────────────── v0.21.4 Installed Parsers ───────────── v2.8.3 Installed Preferences ───────── v1.4.3 Installed PrecompileTools ───── v1.3.2 Installed JSONFBCModels ─────── v1.0.0 Installed AbstractFBCModels ─── v1.3.0 Installed PikaParser ────────── v0.6.1 Updating `~/.julia/environments/v1.13/Project.toml` [475c1105] + JSONFBCModels v1.0.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [5a4f3dfa] + AbstractFBCModels v1.3.0 [ffbed154] + DocStringExtensions v0.9.5 [682c06a0] + JSON v0.21.4 [475c1105] + JSONFBCModels v1.0.0 [69de0a69] + Parsers v2.8.3 [3bbf5609] + PikaParser v0.6.1 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates 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 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [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 v8.14.1+1 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.7.15 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 Installation completed after 1.59s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 2877.1 ms ✓ TestEnv 1 dependency successfully precompiled in 4 seconds. 26 already precompiled. Precompiling package dependencies... Precompilation completed after 51.43s ################################################################################ # Testing # Testing JSONFBCModels Status `/tmp/jl_gkDAE9/Project.toml` [5a4f3dfa] AbstractFBCModels v1.3.0 [ffbed154] DocStringExtensions v0.9.5 [682c06a0] JSON v0.21.4 [475c1105] JSONFBCModels v1.0.0 [3bbf5609] PikaParser v0.6.1 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_gkDAE9/Manifest.toml` [5a4f3dfa] AbstractFBCModels v1.3.0 [ffbed154] DocStringExtensions v0.9.5 [682c06a0] JSON v0.21.4 [475c1105] JSONFBCModels v1.0.0 [69de0a69] Parsers v2.8.3 [3bbf5609] PikaParser v0.6.1 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates 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 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [fa267f1f] TOML v1.0.3 [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 v8.14.1+1 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.7.15 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.1+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 Testing Running tests... reaction_gene_products_available should return Union{Nothing, Bool}: Test Failed at /home/pkgeval/.julia/packages/AbstractFBCModels/bQECn/src/testing.jl:171 Expression: all return types of reaction_gene_products_available(JSONFBCModel, String, Function) are subtypes of Union{Nothing, Bool} Stacktrace: [1] macro expansion @ ~/.julia/packages/AbstractFBCModels/bQECn/src/testing.jl:171 [inlined] [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1858 [inlined] [3] (::AbstractFBCModels.var"#rt#run_fbcmodel_type_tests##0")(::Function, ::Type, ::Type, ::Vararg{Type}) @ AbstractFBCModels ~/.julia/packages/AbstractFBCModels/bQECn/src/testing.jl:171 reaction_gene_association_dnf should return Union{Nothing, Vector{Vector{String}}}: Test Failed at /home/pkgeval/.julia/packages/AbstractFBCModels/bQECn/src/testing.jl:171 Expression: all return types of reaction_gene_association_dnf(JSONFBCModel, String) are subtypes of Union{Nothing, Vector{Vector{String}}} Stacktrace: [1] macro expansion @ ~/.julia/packages/AbstractFBCModels/bQECn/src/testing.jl:171 [inlined] [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1858 [inlined] [3] (::AbstractFBCModels.var"#rt#run_fbcmodel_type_tests##0")(::Function, ::Type, ::Type, ::Vararg{Type}) @ AbstractFBCModels ~/.julia/packages/AbstractFBCModels/bQECn/src/testing.jl:171 metabolite_formula should return Union{Nothing, Dict{String, Int64}}: Test Failed at /home/pkgeval/.julia/packages/AbstractFBCModels/bQECn/src/testing.jl:171 Expression: all return types of metabolite_formula(JSONFBCModel, String) are subtypes of Union{Nothing, Dict{String, Int64}} Stacktrace: [1] macro expansion @ ~/.julia/packages/AbstractFBCModels/bQECn/src/testing.jl:171 [inlined] [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1858 [inlined] [3] (::AbstractFBCModels.var"#rt#run_fbcmodel_type_tests##0")(::Function, ::Type, ::Type, ::Vararg{Type}) @ AbstractFBCModels ~/.julia/packages/AbstractFBCModels/bQECn/src/testing.jl:171 Test Summary: | Pass Fail Total Time JSONFBCModels tests | 76397 3 76400 45.7s Model type JSONFBCModel properties | 30 3 33 6.1s reactions should return Vector{String} | 1 1 0.3s n_reactions should return Int64 | 1 1 0.0s metabolites should return Vector{String} | 1 1 0.0s n_metabolites should return Int64 | 1 1 0.0s genes should return Vector{String} | 1 1 0.0s n_genes should return Int64 | 1 1 0.0s couplings should return Vector{String} | 1 1 0.0s n_couplings should return Int64 | 1 1 0.0s stoichiometry should return SparseArrays.SparseMatrixCSC{Float64, Int64} | 1 1 0.2s coupling should return SparseArrays.SparseMatrixCSC{Float64, Int64} | 1 1 0.0s bounds should return Tuple{Vector{Float64}, Vector{Float64}} | 1 1 0.0s coupling_bounds should return Tuple{Vector{Float64}, Vector{Float64}} | 1 1 0.0s objective should return SparseArrays.SparseVector{Float64, Int64} | 1 1 0.0s balance should return SparseArrays.SparseVector{Float64, Int64} | 1 1 0.0s reaction_stoichiometry should return Dict{String, Float64} | 1 1 0.1s reaction_gene_products_available should return Union{Nothing, Bool} | 1 1 5.2s reaction_gene_association_dnf should return Union{Nothing, Vector{Vector{String}}} | 1 1 0.0s reaction_name should return Union{Nothing, String} | 1 1 0.0s reaction_annotations should return Dict{String, Vector{String}} | 1 1 0.0s reaction_notes should return Dict{String, Vector{String}} | 1 1 0.0s metabolite_formula should return Union{Nothing, Dict{String, Int64}} | 1 1 0.0s metabolite_charge should return Union{Nothing, Int64} | 1 1 0.0s metabolite_compartment should return Union{Nothing, String} | 1 1 0.0s metabolite_name should return Union{Nothing, String} | 1 1 0.0s metabolite_annotations should return Dict{String, Vector{String}} | 1 1 0.0s metabolite_notes should return Dict{String, Vector{String}} | 1 1 0.0s gene_name should return Union{Nothing, String} | 1 1 0.0s gene_annotations should return Dict{String, Vector{String}} | 1 1 0.0s gene_notes should return Dict{String, Vector{String}} | 1 1 0.0s coupling_weights should return Dict{String, Float64} | 1 1 0.0s coupling_name should return Union{Nothing, String} | 1 1 0.0s coupling_annotations should return Dict{String, Vector{String}} | 1 1 0.0s coupling_notes should return Dict{String, Vector{String}} | 1 1 0.0s Model `e_coli_core' of type JSONFBCModel | 1312 1312 25.7s Model `iJO1366' of type JSONFBCModel | 36638 36638 2.6s Model `iML1515' of type JSONFBCModel | 38381 38381 2.7s Test the expected contents of iML1515.json | 24 24 1.5s Miscellaneous tests | 2 2 0.4s Corner cases | 10 10 0.5s RNG of the outermost testset: Random.Xoshiro(0xcbd5b25ed7c27bfe, 0x2b4a035fa09cb455, 0xd036b45f331a80a7, 0x39e603dffdc1448f, 0xf40f5d79a965fc29) ERROR: LoadError: Some tests did not pass: 76397 passed, 3 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/JSONFBCModels/UUJ0L/test/runtests.jl:6 Testing failed after 56.86s ERROR: LoadError: Package JSONFBCModels errored during testing Stacktrace: [1] pkgerror(::String, ::Vararg{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:2661 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2510 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:538 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:168 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:311 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:320 [12] _start() @ Base ./client.jl:553 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 142.69s: package has test failures