Package evaluation of DifferentiableMetabolism on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T14:46:28.495 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.94s ################################################################################ # Installation # Installing DifferentiableMetabolism... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [9677e053] + DifferentiableMetabolism v0.3.0 Updating `~/.julia/environments/v1.11/Manifest.toml` [5a4f3dfa] + AbstractFBCModels v1.3.0 [6e4b80f9] + BenchmarkTools v1.6.0 [babc4406] + COBREXA v2.8.0 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.16.0 [5515826b] + ConstraintTrees v1.9.0 [187b0558] + ConstructionBase v1.5.8 [864edb3b] + DataStructures v0.18.22 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [9677e053] + DifferentiableMetabolism v0.3.0 [ffbed154] + DocStringExtensions v0.9.4 [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 v1.14.2 [4076af6c] + JuMP v1.25.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.15 [b8f27783] + MathOptInterface v1.38.1 [d8a4904e] + MutableArithmetics v1.6.4 [77ba4419] + NaNMath v1.1.3 [bac558e1] + OrderedCollections v1.8.0 [69de0a69] + Parsers v2.8.1 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [7e49a35a] + RuntimeGeneratedFunctions v0.5.13 [276daf66] + SpecialFunctions v2.5.0 [860ef19b] + StableRNGs v1.0.2 [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 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg 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 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.11.0 [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 v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+2 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 4.43s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 71.21s ################################################################################ # Testing # Testing DifferentiableMetabolism Status `/tmp/jl_tubYg2/Project.toml` [5a4f3dfa] AbstractFBCModels v1.3.0 [babc4406] COBREXA v2.8.0 [13f3f980] CairoMakie v0.13.2 [61c947e1] Clarabel v0.10.0 [5515826b] ConstraintTrees v1.9.0 [9677e053] DifferentiableMetabolism v0.3.0 [ffbed154] DocStringExtensions v0.9.4 [eb9bf01b] FastDifferentiation v0.4.4 [475c1105] JSONFBCModels v1.0.0 [4076af6c] JuMP v1.25.0 [6dd1b50a] Tulip v0.9.6 [f43a241f] Downloads v1.6.0 [37e2e46d] LinearAlgebra v1.11.0 [2f01184e] SparseArrays v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_tubYg2/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 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[29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [efcefdf7] PCRE2_jll v10.42.0+1 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Precompiling Tulip... 16219.2 ms ✓ Tulip 1 dependency successfully precompiled in 18 seconds. 75 already precompiled. Precompiling Clarabel... 1369.5 ms ✓ HSL_jll 4700.4 ms ✓ Pardiso 8345.5 ms ✓ HSL 178333.5 ms ✓ Clarabel 4 dependencies successfully precompiled in 194 seconds. 80 already precompiled. ------------------------------------------------------------- Clarabel.jl v0.10.0 - Clever Acronym (c) Paul Goulart University of Oxford, 2022 ------------------------------------------------------------- problem: variables = 6 constraints = 19 nnz(P) = 6 nnz(A) = 27 cones (total) = 2 : Zero = 1, numel = 5 : Nonnegative = 1, numel = 14 settings: linear algebra: direct / qdldl, precision: Float64 max iter = 200, time limit = Inf, max step = 0.990 tol_feas = 1.0e-08, tol_gap_abs = 1.0e-08, tol_gap_rel = 1.0e-08, static reg : on, ϵ1 = 1.0e-08, ϵ2 = 4.9e-32 dynamic reg: on, ϵ = 1.0e-13, δ = 2.0e-07 iter refine: on, reltol = 1.0e-13, abstol = 1.0e-12, max iter = 10, stop ratio = 5.0 equilibrate: on, min_scale = 1.0e-04, max_scale = 1.0e+04 max iter = 10 iter pcost dcost gap pres dres k/t μ step --------------------------------------------------------------------------------------------- 0 8.1662e+04 -2.1285e+06 2.71e+01 1.72e-01 1.29e-16 1.00e+00 4.10e+05 ------ 1 9.3859e+01 -2.2566e+05 2.41e+03 7.83e-03 2.99e-16 1.13e+04 2.44e+04 9.90e-01 2 1.7010e+01 -1.8788e+04 1.11e+03 6.26e-04 2.05e-16 1.35e+02 2.42e+03 9.03e-01 3 1.4683e+01 -5.1608e+02 3.61e+01 1.83e-05 3.47e-15 2.33e+01 9.30e+01 9.73e-01 4 1.4253e+01 -1.4370e+01 2.01e+00 9.86e-07 5.56e-15 1.25e+00 5.05e+00 9.46e-01 5 1.1230e+01 5.0752e+00 1.21e+00 9.61e-08 4.89e-16 2.62e-01 9.65e-01 9.90e-01 6 1.1008e+01 1.0644e+01 3.42e-02 1.11e-09 6.40e-17 1.09e-02 5.32e-02 9.90e-01 7 1.1000e+01 1.0982e+01 1.68e-03 1.16e-11 7.68e-17 5.39e-04 2.50e-03 9.90e-01 8 1.1000e+01 1.1000e+01 2.14e-05 1.08e-13 5.50e-12 6.88e-06 3.17e-05 9.90e-01 9 1.1000e+01 1.1000e+01 2.15e-07 1.05e-15 1.14e-13 6.91e-08 3.18e-07 9.90e-01 10 1.1000e+01 1.1000e+01 2.15e-09 5.09e-17 1.87e-15 6.91e-10 3.18e-09 9.90e-01 --------------------------------------------------------------------------------------------- Terminated with status = solved solve time = 23.9s Precompiling JSONFBCModels... 7869.7 ms ✓ JSONFBCModels 1 dependency successfully precompiled in 8 seconds. 31 already precompiled. Precompiling CairoMakie... 1658.1 ms ✓ StructArrays → StructArraysStaticArraysExt 122944.4 ms ✓ TiffImages 1852.1 ms ✓ FilePaths 10125.0 ms ✓ JpegTurbo 9525.2 ms ✓ Sixel 4397.0 ms ✓ OpenEXR 6499.1 ms ✓ Netpbm 4164.8 ms ✓ Distributions → DistributionsChainRulesCoreExt 43641.1 ms ✓ WebP 9813.2 ms ✓ KernelDensity 412185.8 ms ✓ Makie 258113.0 ms ✓ CairoMakie 12 dependencies successfully precompiled in 890 seconds. 261 already precompiled. Precompiling DistributionsTestExt... 3889.3 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 5 seconds. 48 already precompiled. ┌ Warning: Assignment to `sens` in soft scope is ambiguous because a global variable by the same name exists: `sens` will be treated as a new local. Disambiguate by using `local sens` to suppress this warning or `global sens` to assign to the existing global variable. └ @ ~/.julia/packages/DifferentiableMetabolism/E8ATo/docs/src/3-parameter-estimation.jl:138 Test Summary: | Pass Total Time DifferentiableMetabolism tests | 56 56 30m56.9s Testing DifferentiableMetabolism tests passed Testing completed after 1867.14s PkgEval succeeded after 1966.85s