Package evaluation of ElementaryFluxModes on Julia 1.12.0-DEV.2153 (83dcbd426d*) started at 2025-03-31T11:48:53.674 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.28s ################################################################################ # Installation # Installing ElementaryFluxModes... Resolving package versions... Installed RowEchelon ──────────────── v0.2.1 Installed IrrationalConstants ─────── v0.2.4 Installed DiffResults ─────────────── v1.1.0 Installed DiffRules ───────────────── v1.15.1 Installed JSON3 ───────────────────── v1.14.2 Installed JSON ────────────────────── v0.21.4 Installed Preferences ─────────────── v1.4.3 Installed MutableArithmetics ──────── v1.6.4 Installed Bzip2_jll ───────────────── v1.0.9+0 Installed Parsers ─────────────────── v2.8.1 Installed CodecBzip2 ──────────────── v0.8.5 Installed RuntimeGeneratedFunctions ─ v0.5.13 Installed SpecialFunctions ────────── v2.5.0 Installed BenchmarkTools ──────────── v1.6.0 Installed StaticArrays ────────────── v1.9.13 Installed NaNMath ─────────────────── v1.1.2 Installed StaticArraysCore ────────── v1.4.3 Installed JLLWrappers ─────────────── v1.7.0 Installed OrderedCollections ──────── v1.8.0 Installed PrecompileTools ─────────── v1.3.0 Installed TranscodingStreams ──────── v0.11.3 Installed Statistics ──────────────── v1.11.1 Installed CommonSubexpressions ────── v0.3.1 Installed ForwardDiff ─────────────── v0.10.38 Installed ElementaryFluxModes ─────── v1.0.0 Installed DataStructures ──────────── v0.18.22 Installed LogExpFunctions ─────────── v0.3.29 Installed MacroTools ──────────────── v0.5.15 Installed Compat ──────────────────── v4.16.0 Installed OpenSpecFun_jll ─────────── v0.5.6+0 Installed FastDifferentiation ─────── v0.4.4 Installed ExprTools ───────────────── v0.1.10 Installed CodecZlib ───────────────── v0.7.8 Installed JuMP ────────────────────── v1.25.0 Installed DocStringExtensions ─────── v0.9.4 Installed StructTypes ─────────────── v1.11.0 Installed MathOptInterface ────────── v1.38.0 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Bzip2 503.5 KiB Updating `~/.julia/environments/v1.12/Project.toml` [89210afb] + ElementaryFluxModes v1.0.0 Updating `~/.julia/environments/v1.12/Manifest.toml` [6e4b80f9] + BenchmarkTools v1.6.0 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.16.0 [864edb3b] + DataStructures v0.18.22 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [ffbed154] + DocStringExtensions v0.9.4 [89210afb] + ElementaryFluxModes v1.0.0 [e2ba6199] + ExprTools v0.1.10 [eb9bf01b] + FastDifferentiation v0.4.4 ⌅ [f6369f11] + ForwardDiff v0.10.38 [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 v0.5.15 [b8f27783] + MathOptInterface v1.38.0 [d8a4904e] + MutableArithmetics v1.6.4 [77ba4419] + NaNMath v1.1.2 [bac558e1] + OrderedCollections v1.8.0 [69de0a69] + Parsers v2.8.1 [aea7be01] + PrecompileTools v1.3.0 [21216c6a] + Preferences v1.4.3 [af85af4c] + RowEchelon v0.2.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.13 [276daf66] + SpecialFunctions v2.5.0 [90137ffa] + StaticArrays v1.9.13 [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 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [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 [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 [2f01184e] + SparseArrays v1.12.0 [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 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+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 8.68s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 6993.4 ms ✓ TestEnv 1 dependency successfully precompiled in 9 seconds. 25 already precompiled. Precompiling package dependencies... ERROR: LoadError: The following 1 direct dependency failed to precompile: DifferentiableMetabolism Failed to precompile DifferentiableMetabolism [9677e053-0fc1-49e6-98a8-2ad3a1525e54] to "/home/pkgeval/.julia/compiled/v1.12/DifferentiableMetabolism/jl_lN2s0Q". ERROR: LoadError: cannot declare DifferentiableMetabolism.differentiate_prepare_kkt public; it is already declared exported Stacktrace: [1] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:304 [2] top-level scope @ ~/.julia/packages/DifferentiableMetabolism/yELl2/src/DifferentiableMetabolism.jl:44 [3] include(mod::Module, _path::String) @ Base ./Base.jl:303 [4] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base ./loading.jl:3015 [5] top-level scope @ stdin:5 [6] eval(m::Module, e::Any) @ Core ./boot.jl:489 [7] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2861 [8] include_string @ ./loading.jl:2871 [inlined] [9] exec_options(opts::Base.JLOptions) @ Base ./client.jl:326 [10] _start() @ Base ./client.jl:560 in expression starting at /home/pkgeval/.julia/packages/DifferentiableMetabolism/yELl2/src/public_api.jl:19 in expression starting at /home/pkgeval/.julia/packages/DifferentiableMetabolism/yELl2/src/DifferentiableMetabolism.jl:19 in expression starting at stdin: in expression starting at /PkgEval.jl/scripts/precompile.jl:37 Precompilation failed after 2006.65s ################################################################################ # Testing # Testing ElementaryFluxModes Status `/tmp/jl_Mbp9Cl/Project.toml` [5a4f3dfa] AbstractFBCModels v1.3.0 [babc4406] COBREXA v2.8.0 [13f3f980] CairoMakie v0.13.2 [5515826b] ConstraintTrees v1.9.0 ⌅ [9677e053] DifferentiableMetabolism v0.2.0 [ffbed154] DocStringExtensions v0.9.4 [89210afb] ElementaryFluxModes v1.0.0 [eb9bf01b] FastDifferentiation v0.4.4 [682c06a0] JSON v0.21.4 [475c1105] JSONFBCModels v1.0.0 [4076af6c] JuMP v1.25.0 [af85af4c] RowEchelon v0.2.1 [6dd1b50a] Tulip v0.9.6 [37e2e46d] LinearAlgebra v1.12.0 [2f01184e] SparseArrays v1.12.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_Mbp9Cl/Manifest.toml` [14f7f29c] AMD v0.5.3 [5a4f3dfa] AbstractFBCModels v1.3.0 [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.3.0 [35492f91] AdaptivePredicates v1.2.0 [66dad0bd] AliasTables v1.1.3 [27a7e980] Animations v0.4.2 [67c07d97] Automa v1.1.0 [13072b0f] AxisAlgorithms v1.1.0 [39de3d68] AxisArrays v0.4.7 [6e4b80f9] BenchmarkTools v1.6.0 [fa961155] CEnum v0.5.0 [babc4406] COBREXA v2.8.0 [159f3aea] Cairo v1.1.1 [13f3f980] CairoMakie v0.13.2 [d360d2e6] ChainRulesCore v1.25.1 [523fee87] CodecBzip2 v0.8.5 [944b1d66] CodecZlib v0.7.8 [a2cac450] ColorBrewer v0.4.1 [35d6a980] ColorSchemes v3.29.0 [3da002f7] ColorTypes v0.12.0 [c3611d14] ColorVectorSpace v0.11.0 [5ae59095] Colors v0.13.0 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.16.0 [5515826b] ConstraintTrees v1.9.0 [187b0558] ConstructionBase v1.5.8 [d38c429a] Contour v0.6.3 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] 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Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Precompiling packages... Info Given DifferentiableMetabolism was explicitly requested, output will be shown live  ERROR: LoadError: cannot declare DifferentiableMetabolism.differentiate_prepare_kkt public; it is already declared exported Stacktrace:  [1] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:304  [2] top-level scope  @ ~/.julia/packages/DifferentiableMetabolism/yELl2/src/DifferentiableMetabolism.jl:44  [3] include(mod::Module, _path::String)  @ Base ./Base.jl:303  [4] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3015  [5] top-level scope  @ stdin:5  [6] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [7] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2861  [8] include_string  @ ./loading.jl:2871 [inlined]  [9] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:326  [10] _start()  @ Base ./client.jl:560 in expression starting at /home/pkgeval/.julia/packages/DifferentiableMetabolism/yELl2/src/public_api.jl:19 in expression starting at /home/pkgeval/.julia/packages/DifferentiableMetabolism/yELl2/src/DifferentiableMetabolism.jl:19 in expression starting at stdin:5 ✗ DifferentiableMetabolism 0 dependencies successfully precompiled in 24 seconds. 81 already precompiled. ERROR: LoadError: The following 1 direct dependency failed to precompile: DifferentiableMetabolism Failed to precompile DifferentiableMetabolism [9677e053-0fc1-49e6-98a8-2ad3a1525e54] to "/home/pkgeval/.julia/compiled/v1.12/DifferentiableMetabolism/jl_3XDGmR". ERROR: LoadError: cannot declare DifferentiableMetabolism.differentiate_prepare_kkt public; it is already declared exported Stacktrace: [1] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:304 [2] top-level scope @ ~/.julia/packages/DifferentiableMetabolism/yELl2/src/DifferentiableMetabolism.jl:44 [3] include(mod::Module, _path::String) @ Base ./Base.jl:303 [4] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base ./loading.jl:3015 [5] top-level scope @ stdin:5 [6] eval(m::Module, e::Any) @ Core ./boot.jl:489 [7] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2861 [8] include_string @ ./loading.jl:2871 [inlined] [9] exec_options(opts::Base.JLOptions) @ Base ./client.jl:326 [10] _start() @ Base ./client.jl:560 in expression starting at /home/pkgeval/.julia/packages/DifferentiableMetabolism/yELl2/src/public_api.jl:19 in expression starting at /home/pkgeval/.julia/packages/DifferentiableMetabolism/yELl2/src/DifferentiableMetabolism.jl:19 in expression starting at stdin: in expression starting at /home/pkgeval/.julia/packages/ElementaryFluxModes/MPIp7/test/runtests.jl:9 Testing failed after 43.74s ERROR: LoadError: Package ElementaryFluxModes errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/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/v1.12/Pkg/src/Operations.jl:2365 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2220 [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/v1.12/Pkg/src/API.jl:486 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/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:303 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:328 [12] _start() @ Base ./client.jl:560 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 2170.03s: package fails to precompile