Package evaluation to test ElementaryFluxModes on Julia 1.10.10 (c8be17dcfd*) started at 2026-02-02T19:06:13.559 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.10` Set-up completed after 5.12s ################################################################################ # Installation # Installing ElementaryFluxModes... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [89210afb] + ElementaryFluxModes v1.0.0 Updating `~/.julia/environments/v1.10/Manifest.toml` [6e4b80f9] + BenchmarkTools v1.6.3 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.18.1 [864edb3b] + DataStructures v0.19.3 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [ffbed154] + DocStringExtensions v0.9.5 [89210afb] + ElementaryFluxModes v1.0.0 [e2ba6199] + ExprTools v0.1.10 [eb9bf01b] + FastDifferentiation v0.4.5 [f6369f11] + ForwardDiff v1.3.2 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.4.0 [4076af6c] + JuMP v1.29.4 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [b8f27783] + MathOptInterface v1.49.0 [d8a4904e] + MutableArithmetics v1.6.7 [77ba4419] + NaNMath v1.1.3 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.5.1 [af85af4c] + RowEchelon v0.2.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.17 [276daf66] + SpecialFunctions v2.6.1 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [ec057cc2] + StructUtils v2.6.2 [3bb67fe8] + TranscodingStreams v0.11.3 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [b77e0a4c] + InteractiveUtils [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [de0858da] + Printf [9abbd945] + Profile [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [fa267f1f] + TOML v1.0.3 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [4536629a] + OpenBLAS_jll v0.3.23+5 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+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 9.68s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/h9a3r/src/julia-1.9/activate_set.jl:63 ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ Unsatisfiable requirements detected for package DifferentiableMetabolism [9677e053]: │ DifferentiableMetabolism [9677e053] log: │ ├─possible versions are: 0.1.0-0.5.0 or uninstalled │ ├─restricted to versions 0.2 by project [c19d69cd], leaving only versions: 0.2.0 │ │ └─project [c19d69cd] log: │ │ ├─possible versions are: 0.0.0 or uninstalled │ │ └─project [c19d69cd] is fixed to version 0.0.0 │ └─restricted by compatibility requirements with SparseArrays [2f01184e] to versions: [0.1.0-0.1.1, 0.4.0-0.5.0] or uninstalled — no versions left │ └─SparseArrays [2f01184e] log: │ ├─possible versions are: 1.10.0 or uninstalled │ └─restricted to versions 1 by project [c19d69cd], leaving only versions: 1.10.0 │ └─project [c19d69cd] log: see above │ Stacktrace: │ [1] propagate_constraints!(graph::Pkg.Resolve.Graph, sources::Set{Int64}; log_events::Bool) │ @ Pkg.Resolve /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Resolve/graphtype.jl:1072 │ [2] propagate_constraints! (repeats 2 times) │ @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Resolve/graphtype.jl:1008 [inlined] │ [3] simplify_graph!(graph::Pkg.Resolve.Graph, sources::Set{Int64}; clean_graph::Bool) │ @ Pkg.Resolve /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Resolve/graphtype.jl:1533 │ [4] simplify_graph! (repeats 2 times) │ @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Resolve/graphtype.jl:1532 [inlined] │ [5] resolve_versions!(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, julia_version::VersionNumber, installed_only::Bool) │ @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:414 │ [6] up(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, level::Pkg.Types.UpgradeLevel; skip_writing_project::Bool, preserve::Nothing) │ @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1553 │ [7] up(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; level::Pkg.Types.UpgradeLevel, mode::Pkg.Types.PackageMode, preserve::Nothing, update_registry::Bool, skip_writing_project::Bool, kwargs::@Kwargs{io::Base.DevNull}) │ @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:351 │ [8] up │ @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:326 [inlined] │ [9] up │ @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:164 [inlined] │ [10] #resolve#143 │ @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:357 [inlined] │ [11] resolve │ @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:356 [inlined] │ [12] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/h9a3r/src/julia-1.9/activate_set.jl:68 │ [13] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/h9a3r/src/julia-1.9/activate_set.jl:9 │ [14] (::var"#6#8")() │ @ Main /PkgEval.jl/scripts/precompile.jl:21 │ [15] capture_pkg_output(f::var"#6#8"; suppress::Bool) │ @ Main /PkgEval.jl/scripts/common.jl:55 │ [16] suppress_pkg_output(f::Function) │ @ Main /PkgEval.jl/scripts/common.jl:35 │ [17] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:19 │ [18] include(mod::Module, _path::String) │ @ Base ./Base.jl:495 │ [19] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:316 │ [20] _start() │ @ Base ./client.jl:550 └ @ Main /PkgEval.jl/scripts/precompile.jl:24 Activating project at `~/.julia/environments/v1.10` Precompiling package dependencies... Precompiling packages... 14768.8 ms ✓ ElementaryFluxModes 1 dependency successfully precompiled in 17 seconds. 45 already precompiled. Precompilation completed after 31.59s ################################################################################ # Testing # Testing ElementaryFluxModes ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1829 Testing failed after 6.81s ERROR: LoadError: Unsatisfiable requirements detected for package DifferentiableMetabolism [9677e053]: DifferentiableMetabolism [9677e053] log: ├─possible versions are: 0.1.0-0.5.0 or uninstalled ├─restricted to versions 0.2 by project [86ba6030], leaving only versions: 0.2.0 │ └─project [86ba6030] log: │ ├─possible versions are: 0.0.0 or uninstalled │ └─project [86ba6030] is fixed to version 0.0.0 └─restricted by compatibility requirements with SparseArrays [2f01184e] to versions: [0.1.0-0.1.1, 0.4.0-0.5.0] or uninstalled — no versions left └─SparseArrays [2f01184e] log: ├─possible versions are: 1.10.0 or uninstalled └─restricted to versions 1 by project [86ba6030], leaving only versions: 1.10.0 └─project [86ba6030] log: see above Stacktrace: [1] propagate_constraints!(graph::Pkg.Resolve.Graph, sources::Set{Int64}; log_events::Bool) @ Pkg.Resolve /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Resolve/graphtype.jl:1072 [2] propagate_constraints! (repeats 2 times) @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Resolve/graphtype.jl:1008 [inlined] [3] simplify_graph!(graph::Pkg.Resolve.Graph, sources::Set{Int64}; clean_graph::Bool) @ Pkg.Resolve /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Resolve/graphtype.jl:1533 [4] simplify_graph! (repeats 2 times) @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Resolve/graphtype.jl:1532 [inlined] [5] resolve_versions!(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, julia_version::VersionNumber, installed_only::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:414 [6] up(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, level::Pkg.Types.UpgradeLevel; skip_writing_project::Bool, preserve::Nothing) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1553 [7] up(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; level::Pkg.Types.UpgradeLevel, mode::Pkg.Types.PackageMode, preserve::Nothing, update_registry::Bool, skip_writing_project::Bool, kwargs::@Kwargs{io::Base.DevNull}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:351 [8] up @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:326 [inlined] [9] up @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:164 [inlined] [10] #resolve#143 @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:357 [inlined] [11] resolve @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:356 [inlined] [12] (::Pkg.Operations.var"#117#122"{String, Bool, Bool, Bool, Pkg.Operations.var"#130#134"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, Pkg.Types.PackageSpec}, Pkg.Types.PackageSpec})() @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1831 [13] with_temp_env(fn::Pkg.Operations.var"#117#122"{String, Bool, Bool, Bool, Pkg.Operations.var"#130#134"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, Pkg.Types.PackageSpec}, Pkg.Types.PackageSpec}, temp_env::String) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1721 [14] (::Pkg.Operations.var"#115#120"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#130#134"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, Pkg.Types.PackageSpec}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, Pkg.Types.Project, String})(tmp::String) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1810 [15] mktempdir(fn::Pkg.Operations.var"#115#120"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#130#134"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, Pkg.Types.PackageSpec}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, Pkg.Types.Project, String}, parent::String; prefix::String) @ Base.Filesystem ./file.jl:766 [16] mktempdir(fn::Function, parent::String) @ Base.Filesystem ./file.jl:762 [17] mktempdir @ ./file.jl:762 [inlined] [18] sandbox(fn::Function, ctx::Pkg.Types.Context, target::Pkg.Types.PackageSpec, target_path::String, sandbox_path::String, sandbox_project_override::Pkg.Types.Project; preferences::Dict{String, Any}, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1768 [19] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.10/Pkg/src/Operations.jl:1971 [20] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined] [21] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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::Base.PipeEndpoint}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444 [22] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159 [23] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined] [24] #test#74 @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined] [25] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 caused by: empty intersection between JSON@1.4.0 and project compatibility 0.21 Stacktrace: [1] resolve_versions!(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}, julia_version::VersionNumber, installed_only::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:396 [2] up(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, level::Pkg.Types.UpgradeLevel; skip_writing_project::Bool, preserve::Nothing) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1553 [3] up(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; level::Pkg.Types.UpgradeLevel, mode::Pkg.Types.PackageMode, preserve::Nothing, update_registry::Bool, skip_writing_project::Bool, kwargs::@Kwargs{io::Base.DevNull}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:351 [4] up @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:326 [inlined] [5] up @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:164 [inlined] [6] #resolve#143 @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:357 [inlined] [7] resolve @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:356 [inlined] [8] (::Pkg.Operations.var"#117#122"{String, Bool, Bool, Bool, Pkg.Operations.var"#130#134"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, Pkg.Types.PackageSpec}, Pkg.Types.PackageSpec})() @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1823 [9] with_temp_env(fn::Pkg.Operations.var"#117#122"{String, Bool, Bool, Bool, Pkg.Operations.var"#130#134"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, Pkg.Types.PackageSpec}, Pkg.Types.PackageSpec}, temp_env::String) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1721 [10] (::Pkg.Operations.var"#115#120"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#130#134"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, Pkg.Types.PackageSpec}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, Pkg.Types.Project, String})(tmp::String) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1810 [11] mktempdir(fn::Pkg.Operations.var"#115#120"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#130#134"{Bool, Cmd, Cmd, Nothing, Pkg.Types.Context, Vector{Tuple{String, Base.Process}}, String, Pkg.Types.PackageSpec}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, Pkg.Types.Project, String}, parent::String; prefix::String) @ Base.Filesystem ./file.jl:766 [12] mktempdir(fn::Function, parent::String) @ Base.Filesystem ./file.jl:762 [13] mktempdir @ ./file.jl:762 [inlined] [14] sandbox(fn::Function, ctx::Pkg.Types.Context, target::Pkg.Types.PackageSpec, target_path::String, sandbox_path::String, sandbox_project_override::Pkg.Types.Project; preferences::Dict{String, Any}, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1768 [15] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.10/Pkg/src/Operations.jl:1971 [16] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined] [17] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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::Base.PipeEndpoint}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444 [18] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159 [19] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined] [20] #test#74 @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined] [21] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 PkgEval failed after 60.22s: there were unidentified errors