Package evaluation of ElementaryFluxModes on Julia 1.10.9 (96dc2d8c45*) started at 2025-06-06T16:29:27.858


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 5.05s


################################################################################
# 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 v1.6.0
  [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 v1.0.1
  [92d709cd] + IrrationalConstants v0.2.4
  [692b3bcd] + JLLWrappers v1.7.0
  [682c06a0] + JSON v0.21.4
  [0f8b85d8] + JSON3 v1.14.3
  [4076af6c] + JuMP v1.26.0
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [1914dd2f] + MacroTools v0.5.16
  [b8f27783] + MathOptInterface v1.40.2
  [d8a4904e] + MutableArithmetics v1.6.4
  [77ba4419] + NaNMath v1.1.3
  [bac558e1] + OrderedCollections v1.8.1
  [69de0a69] + Parsers v2.8.3
⌅ [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [af85af4c] + RowEchelon v0.2.1
  [7e49a35a] + RuntimeGeneratedFunctions v0.5.15
  [276daf66] + SpecialFunctions v2.5.1
  [90137ffa] + StaticArrays v1.9.13
  [1e83bf80] + StaticArraysCore v1.4.3
  [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
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [b77e0a4c] + InteractiveUtils
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [a63ad114] + Mmap
  [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+4
  [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 8.16s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...

┌ Warning: Could not use exact versions of packages in manifest, re-resolving
└ @ TestEnv ~/.julia/packages/TestEnv/iS95e/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 SparseArrays [2f01184e]:
│     SparseArrays [2f01184e] log:
│     ├─possible versions are: 1.10.0 or uninstalled
│     ├─restricted to versions 1 by project [367a7d69], leaving only versions: 1.10.0
│     │ └─project [367a7d69] log:
│     │   ├─possible versions are: 0.0.0 or uninstalled
│     │   └─project [367a7d69] is fixed to version 0.0.0
│     └─found to have no compatible versions left with DifferentiableMetabolism [9677e053]
│       └─DifferentiableMetabolism [9677e053] log:
│         ├─possible versions are: 0.1.0-0.3.0 or uninstalled
│         └─restricted to versions 0.2 by project [367a7d69], leaving only versions: 0.2.0
│           └─project [367a7d69] 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/iS95e/src/julia-1.9/activate_set.jl:68
│     [13] activate(pkg::String)
│        @ TestEnv ~/.julia/packages/TestEnv/iS95e/src/julia-1.9/activate_set.jl:9
│     [14] top-level scope
│        @ /PkgEval.jl/scripts/precompile.jl:24
│     [15] include(mod::Module, _path::String)
│        @ Base ./Base.jl:495
│     [16] exec_options(opts::Base.JLOptions)
│        @ Base ./client.jl:323
│     [17] _start()
│        @ Base ./client.jl:557
└ @ Main /PkgEval.jl/scripts/precompile.jl:26
Precompiling package dependencies...
Precompiling packages...
  15728.7 ms  ✓ ElementaryFluxModes
  1 dependency successfully precompiled in 18 seconds. 46 already precompiled.

Precompilation completed after 31.4s


################################################################################
# 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 6.76s

ERROR: LoadError: Unsatisfiable requirements detected for package DifferentiableMetabolism [9677e053]:
 DifferentiableMetabolism [9677e053] log:
 ├─possible versions are: 0.1.0-0.3.0 or uninstalled
 ├─restricted to versions 0.2 by project [ed6dcb48], leaving only versions: 0.2.0
 │ └─project [ed6dcb48] log:
 │   ├─possible versions are: 0.0.0 or uninstalled
 │   └─project [ed6dcb48] is fixed to version 0.0.0
 └─restricted by compatibility requirements with LinearAlgebra [37e2e46d] to versions: 0.1.0-0.1.1 or uninstalled — no versions left
   └─LinearAlgebra [37e2e46d] log:
     ├─possible versions are: 1.10.9 or uninstalled (package in sysimage!)
     └─restricted to versions * by project [ed6dcb48], leaving only versions: 1.10.9
       └─project [ed6dcb48] 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:219
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

caused by: Unsatisfiable requirements detected for package DifferentiableMetabolism [9677e053]:
 DifferentiableMetabolism [9677e053] log:
 ├─possible versions are: 0.1.0-0.3.0 or uninstalled
 ├─restricted to versions 0.2 by project [ed6dcb48], leaving only versions: 0.2.0
 │ └─project [ed6dcb48] log:
 │   ├─possible versions are: 0.0.0 or uninstalled
 │   └─project [ed6dcb48] is fixed to version 0.0.0
 └─restricted by compatibility requirements with LinearAlgebra [37e2e46d] to versions: 0.1.0-0.1.1 or uninstalled — no versions left
   └─LinearAlgebra [37e2e46d] log:
     ├─possible versions are: 1.10.9 or uninstalled (package in sysimage!)
     └─restricted to versions * by project [ed6dcb48], leaving only versions: 1.10.9
       └─project [ed6dcb48] 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:1823
 [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:219

PkgEval failed after 59.35s: there were unidentified errors